diff --git a/actions.txt b/actions.txt new file mode 100644 index 0000000..1482413 --- /dev/null +++ b/actions.txt @@ -0,0 +1,23 @@ +generate_flow_chart_data_older_adults_s1 process_flow_chart_data_older_adults_s1 generate_flow_chart_data_older_adults_s2 process_flow_chart_data_older_adults_s2 generate_flow_chart_data_older_adults_s3 process_flow_chart_data_older_adults_s3 generate_flow_chart_data_older_adults_s4 process_flow_chart_data_older_adults_s4 generate_flow_chart_data_older_adults_s5 process_flow_chart_data_older_adults_s5 generate_flow_chart_data_older_adults_s6 process_flow_chart_data_older_adults_s6 generate_flow_chart_data_older_adults_s7 process_flow_chart_data_older_adults_s7 +generate_flow_chart_data_adults_s1 process_flow_chart_data_adults_s1 generate_flow_chart_data_adults_s2 process_flow_chart_data_adults_s2 generate_flow_chart_data_adults_s3 process_flow_chart_data_adults_s3 generate_flow_chart_data_adults_s4 process_flow_chart_data_adults_s4 generate_flow_chart_data_adults_s5 process_flow_chart_data_adults_s5 generate_flow_chart_data_adults_s6 process_flow_chart_data_adults_s6 generate_flow_chart_data_adults_s7 process_flow_chart_data_adults_s7 +generate_flow_chart_data_children_and_adolescents_s1 process_flow_chart_data_children_and_adolescents_s1 generate_flow_chart_data_children_and_adolescents_s2 process_flow_chart_data_children_and_adolescents_s2 generate_flow_chart_data_children_and_adolescents_s3 process_flow_chart_data_children_and_adolescents_s3 generate_flow_chart_data_children_and_adolescents_s4 process_flow_chart_data_children_and_adolescents_s4 generate_flow_chart_data_children_and_adolescents_s5 process_flow_chart_data_children_and_adolescents_s5 generate_flow_chart_data_children_and_adolescents_s6 process_flow_chart_data_children_and_adolescents_s6 generate_flow_chart_data_children_and_adolescents_s7 process_flow_chart_data_children_and_adolescents_s7 +generate_flow_chart_data_infants_s1 process_flow_chart_data_infants_s1 generate_flow_chart_data_infants_s2 process_flow_chart_data_infants_s2 generate_flow_chart_data_infants_s3 process_flow_chart_data_infants_s3 generate_flow_chart_data_infants_s4 process_flow_chart_data_infants_s4 generate_flow_chart_data_infants_s5 process_flow_chart_data_infants_s5 generate_flow_chart_data_infants_s6 process_flow_chart_data_infants_s6 generate_flow_chart_data_infants_s7 process_flow_chart_data_infants_s7 +extract_household_information_s1 process_household_information_s1 extract_household_information_s2 process_household_information_s2 extract_household_information_s3 process_household_information_s3 extract_household_information_s4 process_household_information_s4 extract_household_information_s5 process_household_information_s5 extract_household_information_s6 process_household_information_s6 extract_household_information_s7 process_household_information_s7 +generate_dataset_older_adults_s1_specific_primary 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analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary analyse_dataset_infants_rsv_ethnicity_hh_comp_s7_sensitive_secondary analyse_dataset_infants_flu_ethnicity_hh_comp_s7_sensitive_secondary analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary analyse_dataset_infants_rsv_ses_hh_comp_s7_sensitive_secondary analyse_dataset_infants_flu_ses_hh_comp_s7_sensitive_secondary analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary analyse_dataset_infants_rsv_full_s7_sensitive_secondary analyse_dataset_infants_flu_full_s7_sensitive_secondary analyse_dataset_infants_overall_and_all_cause_full_s7_sensitive_secondary analyse_dataset_infants_further_rsv_ethnicity_s7_sensitive_secondary analyse_dataset_infants_further_flu_ethnicity_s7_sensitive_secondary analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_sensitive_secondary analyse_dataset_infants_further_rsv_ses_s7_sensitive_secondary analyse_dataset_infants_further_flu_ses_s7_sensitive_secondary analyse_dataset_infants_further_overall_and_all_cause_ses_s7_sensitive_secondary analyse_dataset_infants_further_rsv_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_flu_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_rsv_ethnicity_ses_s7_sensitive_secondary analyse_dataset_infants_further_flu_ethnicity_ses_s7_sensitive_secondary analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_rsv_ses_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_flu_ses_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary analyse_dataset_infants_further_rsv_full_s7_sensitive_secondary analyse_dataset_infants_further_flu_full_s7_sensitive_secondary analyse_dataset_infants_further_overall_and_all_cause_full_s7_sensitive_secondary +describe_cohort_older_adults_s1 describe_cohort_older_adults_s2 describe_cohort_older_adults_s3 describe_cohort_older_adults_s4 describe_cohort_older_adults_s5 describe_cohort_older_adults_s6 describe_cohort_older_adults_s7 +describe_cohort_adults_s1 describe_cohort_adults_s2 describe_cohort_adults_s3 describe_cohort_adults_s4 describe_cohort_adults_s5 describe_cohort_adults_s6 describe_cohort_adults_s7 +describe_cohort_children_and_adolescents_s1 describe_cohort_children_and_adolescents_s2 describe_cohort_children_and_adolescents_s3 describe_cohort_children_and_adolescents_s4 describe_cohort_children_and_adolescents_s5 describe_cohort_children_and_adolescents_s6 describe_cohort_children_and_adolescents_s7 +describe_cohort_infants_s1 describe_cohort_infants_s2 describe_cohort_infants_s3 describe_cohort_infants_s4 describe_cohort_infants_s5 describe_cohort_infants_s6 describe_cohort_infants_s7 +collate_flow_chart_tables_older_adults collate_table1_tables_older_adults collate_rates_tables_older_adults collate_rsv_model_outputs_tables_older_adults collate_flu_model_outputs_tables_older_adults collate_covid_model_outputs_tables_older_adults collate_overall_and_all_cause_model_outputs_tables_older_adults collate_rsv_sensitivity_model_outputs_tables_older_adults collate_flu_sensitivity_model_outputs_tables_older_adults collate_covid_sensitivity_model_outputs_tables_older_adults collate_overall_and_all_cause_sensitivity_model_outputs_tables_older_adults collate_flow_chart_tables_adults collate_table1_tables_adults collate_rates_tables_adults collate_rsv_model_outputs_tables_adults collate_flu_model_outputs_tables_adults collate_covid_model_outputs_tables_adults collate_overall_and_all_cause_model_outputs_tables_adults collate_rsv_sensitivity_model_outputs_tables_adults collate_flu_sensitivity_model_outputs_tables_adults collate_covid_sensitivity_model_outputs_tables_adults collate_overall_and_all_cause_sensitivity_model_outputs_tables_adults collate_flow_chart_tables_children_and_adolescents collate_table1_tables_children_and_adolescents collate_rates_tables_children_and_adolescents collate_rsv_model_outputs_tables_children_and_adolescents collate_flu_model_outputs_tables_children_and_adolescents collate_covid_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_model_outputs_tables_children_and_adolescents collate_rsv_sensitivity_model_outputs_tables_children_and_adolescents collate_flu_sensitivity_model_outputs_tables_children_and_adolescents collate_covid_sensitivity_model_outputs_tables_children_and_adolescents collate_overall_and_all_cause_sensitivity_model_outputs_tables_children_and_adolescents collate_flow_chart_tables_infants collate_table1_tables_infants collate_rates_tables_infants collate_rsv_model_outputs_tables_infants collate_flu_model_outputs_tables_infants collate_covid_model_outputs_tables_infants collate_overall_and_all_cause_model_outputs_tables_infants collate_rsv_sensitivity_model_outputs_tables_infants collate_flu_sensitivity_model_outputs_tables_infants collate_covid_sensitivity_model_outputs_tables_infants collate_overall_and_all_cause_sensitivity_model_outputs_tables_infants + diff --git a/create-project.R b/create-project.R new file mode 100644 index 0000000..58a30a4 --- /dev/null +++ b/create-project.R @@ -0,0 +1,1599 @@ +library('tidyverse') +library('yaml') +library('here') +library('glue') + +# create action functions ---- + +## create comment function ---- +comment <- function(...){ + list_comments <- list(...) + comments <- map(list_comments, ~paste0("## ", ., " ##")) + comments +} + +#splice <- function(...) {list_flatten(lst(...))} + +## create function to convert comment "actions" in a yaml string into proper comments +convert_comment_actions <-function(yaml.txt){ + yaml.txt %>% + str_replace_all("\\\n(\\s*)\\'\\'\\:(\\s*)\\'", "\n\\1") %>% + str_replace_all("([^\\'])\\\n(\\s*)\\#\\#", "\\1\n\n\\2\\#\\#") %>% + str_replace_all("\\#\\#\\'\\\n", "\n") +} + + +## generic action function ---- +action <- function( + name, + run, + arguments=NULL, + needs=NULL, + highly_sensitive=NULL, + moderately_sensitive=NULL, + ... # other arguments / options for special action types +){ + + outputs <- list( + highly_sensitive = highly_sensitive, + moderately_sensitive = moderately_sensitive + ) + outputs[sapply(outputs, is.null)] <- NULL + + action <- list( + run = paste(c(run, arguments), collapse=" "), + needs = needs, + outputs = outputs, + ... = ... + ) + action[sapply(action, is.null)] <- NULL + + action_list <- list(name = action) + names(action_list) <- name + + action_list +} + + +##actions for inclusion/exclusion + +action_inclusion <- function(cohort, season, dates, season_start_date, + season_end_date) { + + splice ( + + action( + name = glue("generate_flow_chart_data_{cohort}_{season}"), + run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/{cohort}_{dates}_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow + -- {cohort} {season_start_date} {season_end_date}"), + arguments = c(cohort, season, dates, season_start_date, season_end_date), + needs = NULL, + highly_sensitive = lst( + dataset = glue("output/flow_chart/{cohort}_{dates}_flow_chart.csv"), + ) + ), + + action( + name = glue("process_flow_chart_data_{cohort}_{season}"), + run = glue("r:latest analysis/cohort_criteria.R {cohort} {season_start_date} {season_end_date}"), + arguments = c(cohort, season, dates, season_start_date, season_end_date), + needs = list(glue("generate_flow_chart_data_{cohort}_{season}")), + highly_sensitive = lst( + cohort = glue("output/flow_chart/flow_chart_processed_{cohort}_{dates}.csv"), + ) + ) + + ) +} + +##household actions + +action_household <- function(season, dates, season_start_date, season_end_date) { + + splice ( + + action( + name = glue("extract_household_information_{season}"), + run = glue("ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_{dates}.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_{dates}.arrow + -- {season_start_date} {season_end_date}"), + arguments = c(season, dates, season_start_date, season_end_date), + needs = NULL, + highly_sensitive = lst( + dataset = glue("output/data/input_household_{dates}.arrow"), + ) + ), + + action( + name = glue("process_household_information_{season}"), + run = glue("r:latest analysis/data_processing_household.R {season_start_date} {season_end_date}"), + arguments = c(season, dates, season_start_date, season_end_date), + needs = list(glue("extract_household_information_{season}")), + highly_sensitive = lst( + arrow = glue("output/data/input_household_processed_{dates}.arrow"), + ) + ) + + ) +} + +##actions for all cohorts/seasons + +action_specified <- function(cohort, season, dates, + codelist_type, investigation_type, + season_start_date, season_end_date){ + + splice( + + action( + name = glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"), + run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow + --dummy-data-file analysis/dummydata/dummyextract_{cohort}_{dates}.arrow + -- {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = NULL, + highly_sensitive = lst( + dataset = glue("output/data/input_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow"), + ) + ), + + action( + name = glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/data_processing.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("generate_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"), + glue("process_household_information_{season}")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_{dates}_{codelist_type}_{investigation_type}.arrow"), + ) + ), + + action( + name = glue("describe_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/report.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/rates/rates_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv"), + ) + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/rsv_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/flu_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/rsv_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/flu_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/rsv_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/flu_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/flu_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/flu_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/rsv_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/flu_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/further_flu_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/further_rsv_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/further_flu_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/further_flu_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/rsv_specific/further_rsv_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/flu_specific/further_flu_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ) + + ) + +} + +##covid actions + +action_covid <- function(cohort, season, dates, codelist_type, + investigation_type, season_start_date, season_end_date) { + + splice( + + action( + name = glue("analyse_dataset_{cohort}_covid_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/covid_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/covid_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/covid_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/covid_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/covid_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/covid_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/further_covid_ethnicity_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}further__covid_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/further_covid_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_covid_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/further_covid_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_covid_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_covid_full_{season}_{codelist_type}_{investigation_type}"), + run = glue("r:latest analysis/covid_specific/further_covid_full_models.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + ) + + ) + +} + +##descriptive actions + +action_descriptive <- function(cohort, season, dates, + codelist_type, investigation_type, + season_start_date, season_end_date) { + + splice( + + action( + name = glue("describe_cohort_{cohort}_{season}"), + run = glue("r:latest analysis/cohort_description.R {cohort} {season_start_date} {season_end_date} sensitive secondary"), + arguments = c(cohort, season, dates, codelist_type, investigation_type, + season_start_date, season_end_date), + needs = list(glue("process_dataset_{cohort}_{season}_sensitive_secondary")), + moderately_sensitive = lst( + csv = glue("output/table1/table1_{cohort}_{dates}.csv")), + ) + + ) + +} + +action_finalise <- function(cohort) { + + splice( + + action( + name = glue("collate_flow_chart_tables_{cohort}"), + run = glue("r:latest analysis/flow_chart_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("process_flow_chart_data_{cohort}_s1"), + glue("process_flow_chart_data_{cohort}_s2"), + glue("process_flow_chart_data_{cohort}_s3"), + glue("process_flow_chart_data_{cohort}_s4"), + glue("process_flow_chart_data_{cohort}_s5"), + glue("process_flow_chart_data_{cohort}_s6"), + glue("process_flow_chart_data_{cohort}_s7")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_flow_chart_collated.csv"), + ) + ), + action( + name = glue("collate_table1_tables_{cohort}"), + run = glue("r:latest analysis/table1_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("describe_dataset_{cohort}_s1_specific_primary"), + glue("describe_dataset_{cohort}_s2_specific_primary"), + glue("describe_dataset_{cohort}_s3_specific_primary"), + glue("describe_dataset_{cohort}_s4_specific_primary"), + glue("describe_dataset_{cohort}_s5_specific_primary"), + glue("describe_dataset_{cohort}_s6_specific_primary"), + glue("describe_dataset_{cohort}_s7_specific_primary"), + glue("describe_dataset_{cohort}_s1_sensitive_primary"), + glue("describe_dataset_{cohort}_s2_sensitive_primary"), + glue("describe_dataset_{cohort}_s3_sensitive_primary"), + glue("describe_dataset_{cohort}_s4_sensitive_primary"), + glue("describe_dataset_{cohort}_s5_sensitive_primary"), + glue("describe_dataset_{cohort}_s6_sensitive_primary"), + glue("describe_dataset_{cohort}_s7_sensitive_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_table1_collated.csv")) + ), + + action( + name = glue("collate_rates_tables_{cohort}"), + run = glue("r:latest analysis/rates_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("process_dataset_{cohort}_s1_specific_primary"), + glue("process_dataset_{cohort}_s2_specific_primary"), + glue("process_dataset_{cohort}_s3_specific_primary"), + glue("process_dataset_{cohort}_s4_specific_primary"), + glue("process_dataset_{cohort}_s5_specific_primary"), + glue("process_dataset_{cohort}_s6_specific_primary"), + glue("process_dataset_{cohort}_s7_specific_primary"), + glue("process_dataset_{cohort}_s1_sensitive_primary"), + glue("process_dataset_{cohort}_s2_sensitive_primary"), + glue("process_dataset_{cohort}_s3_sensitive_primary"), + glue("process_dataset_{cohort}_s4_sensitive_primary"), + glue("process_dataset_{cohort}_s5_sensitive_primary"), + glue("process_dataset_{cohort}_s6_sensitive_primary"), + glue("process_dataset_{cohort}_s7_sensitive_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_rates_collated.csv")) + ), + + action( + name = glue("collate_rsv_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/rsv_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_rsv_ethnicity_s1_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s2_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s3_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s4_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s5_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s6_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s7_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s1_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s2_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s3_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s1_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s2_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s3_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s1_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s2_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s3_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s4_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s5_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s6_specific_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s7_specific_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_rsv_model_outputs_collated.csv")) + ), + + action( + name = glue("collate_flu_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/flu_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_flu_ethnicity_s1_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s2_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s3_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s4_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s5_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s6_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s7_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s1_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s2_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s3_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s1_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s2_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s3_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_flu_full_s1_specific_primary"), + glue("analyse_dataset_{cohort}_flu_full_s2_specific_primary"), + glue("analyse_dataset_{cohort}_flu_full_s3_specific_primary"), + glue("analyse_dataset_{cohort}_flu_full_s4_specific_primary"), + glue("analyse_dataset_{cohort}_flu_full_s5_specific_primary"), + glue("analyse_dataset_{cohort}_flu_full_s6_specific_primary"), + glue("analyse_dataset_{cohort}_flu_full_s7_specific_primary")), + moderately_sensitive = lst( + glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv")) + ), + + action( + name = glue("collate_covid_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/covid_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_covid_ethnicity_s4_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_s5_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_s6_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_s7_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_covid_full_s4_specific_primary"), + glue("analyse_dataset_{cohort}_covid_full_s5_specific_primary"), + glue("analyse_dataset_{cohort}_covid_full_s6_specific_primary"), + glue("analyse_dataset_{cohort}_covid_full_s7_specific_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_covid_model_outputs_collated.csv")) + ), + + action( + name = glue("collate_overall_and_all_cause_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/overall_and_all_cause_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s1_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s2_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s3_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s4_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s5_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s6_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s7_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s1_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s2_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s3_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s1_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s2_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s3_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s4_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s5_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s6_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s7_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s1_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s2_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s3_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s4_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s5_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s6_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s7_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s1_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s2_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s3_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s4_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s5_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s6_specific_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s7_specific_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_overall_and_all_cause_model_outputs_collated.csv")) + ), + + action( + name = glue("collate_rsv_sensitivity_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_rsv_ethnicity_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_rsv_full_s7_sensitive_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_rsv_sensitivity_model_outputs_collated.csv")) + ), + + action( + name = glue("collate_flu_sensitivity_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/flu_sensitivity_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_flu_ethnicity_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_full_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_full_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_full_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_full_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_full_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_full_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_flu_full_s7_sensitive_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_flu_sensitivity_model_outputs_collated.csv")) + ), + + action( + name = glue("collate_covid_sensitivity_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/covid_sensitivity_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_covid_ethnicity_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_full_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_full_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_full_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_covid_full_s7_sensitive_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_covid_sensitivity_model_outputs_collated.csv")) + ), + + action( + name = glue("collate_overall_and_all_cause_sensitivity_model_outputs_tables_{cohort}"), + run = glue("r:latest analysis/overall_and_all_cause_sensitivity_model_outputs_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s1_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s2_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s3_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s4_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s5_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s6_sensitive_primary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s7_sensitive_primary")), + moderately_sensitive = lst( + csv = glue("output/results/collated/{cohort}_overall_and_all_cause_sensitivity_model_outputs_collated.csv")) + ) + ) +} + +# specify project ---- + +## defaults ---- +defaults_list <- lst( + version = "3.0", + expectations= lst(population_size=100000L) +) + +## actions ---- +actions_list <- splice( + + comment("# # # # # # # # # # # # # # # # # # #", + "DO NOT EDIT project.yaml DIRECTLY", + "This file is created by create-project.R", + "Edit and run create-project.R to update the project.yaml", + "# # # # # # # # # # # # # # # # # # #" + ), + + + comment("# # # # # # # # # # # # # # # # # # #", "Pre-server scripts", "# # # # # # # # # # # # # # # # # # #"), + + # doesn't currently work as "project.yaml is not an allowed file type" + # action( + # name = "checkyaml", + # run = "r:latest create-project.R", + # moderately_sensitive = lst( + # project = "project.yaml" + # ) + # ), + + comment("# # # # # # # # # # # # # # # # # # #", "Inclusion/Exclusion Flow Chart Actions: Older Adults", "# # # # # # # # # # # # # # # # # # #"), + + action_inclusion("older_adults", "s1", "2016_2017", "season1_start_date", "season1_end_date"), + action_inclusion("older_adults", "s2", "2017_2018", "season2_start_date", "season2_end_date"), + action_inclusion("older_adults", "s3", "2018_2019", "season3_start_date", "season3_end_date"), + action_inclusion("older_adults", "s4", "2019_2020", "season4_start_date", "season4_end_date"), + action_inclusion("older_adults", "s5", "2020_2021", "season5_start_date", "season5_end_date"), + action_inclusion("older_adults", "s6", "2021_2022", "season6_start_date", "season6_end_date"), + action_inclusion("older_adults", "s7", "2022_2023", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Inclusion/Exclusion Flow Chart Actions: Adults", "# # # # # # # # # # # # # # # # # # #"), + + action_inclusion("adults", "s1", "2016_2017", "season1_start_date", "season1_end_date"), + action_inclusion("adults", "s2", "2017_2018", "season2_start_date", "season2_end_date"), + action_inclusion("adults", "s3", "2018_2019", "season3_start_date", "season3_end_date"), + action_inclusion("adults", "s4", "2019_2020", "season4_start_date", "season4_end_date"), + action_inclusion("adults", "s5", "2020_2021", "season5_start_date", "season5_end_date"), + action_inclusion("adults", "s6", "2021_2022", "season6_start_date", "season6_end_date"), + action_inclusion("adults", "s7", "2022_2023", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Inclusion/Exclusion Flow Chart Actions: Children and Adolescents", "# # # # # # # # # # # # # # # # # # #"), + + action_inclusion("children_and_adolescents", "s1", "2016_2017", "season1_start_date", "season1_end_date"), + action_inclusion("children_and_adolescents", "s2", "2017_2018", "season2_start_date", "season2_end_date"), + action_inclusion("children_and_adolescents", "s3", "2018_2019", "season3_start_date", "season3_end_date"), + action_inclusion("children_and_adolescents", "s4", "2019_2020", "season4_start_date", "season4_end_date"), + action_inclusion("children_and_adolescents", "s5", "2020_2021", "season5_start_date", "season5_end_date"), + action_inclusion("children_and_adolescents", "s6", "2021_2022", "season6_start_date", "season6_end_date"), + action_inclusion("children_and_adolescents", "s7", "2022_2023", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Inclusion/Exclusion Flow Chart Actions: Infants", "# # # # # # # # # # # # # # # # # # #"), + + action_inclusion("infants", "s1", "2016_2017", "season1_start_date", "season1_end_date"), + action_inclusion("infants", "s2", "2017_2018", "season2_start_date", "season2_end_date"), + action_inclusion("infants", "s3", "2018_2019", "season3_start_date", "season3_end_date"), + action_inclusion("infants", "s4", "2019_2020", "season4_start_date", "season4_end_date"), + action_inclusion("infants", "s5", "2020_2021", "season5_start_date", "season5_end_date"), + action_inclusion("infants", "s6", "2021_2022", "season6_start_date", "season6_end_date"), + action_inclusion("infants", "s7", "2022_2023", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Household Information Actions", "# # # # # # # # # # # # # # # # # # #"), + + action_household("s1", "2016_2017", "season1_start_date", "season1_end_date"), + action_household("s2", "2017_2018", "season2_start_date", "season2_end_date"), + action_household("s3", "2018_2019", "season3_start_date", "season3_end_date"), + action_household("s4", "2019_2020", "season4_start_date", "season4_end_date"), + action_household("s5", "2020_2021", "season5_start_date", "season5_end_date"), + action_household("s6", "2021_2022", "season6_start_date", "season6_end_date"), + action_household("s7", "2022_2023", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults, Codelist Type: Specific, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("older_adults", "s1", "2016_2017", "specific", "primary", "season1_start_date", "season1_end_date"), + action_specified("older_adults", "s2", "2017_2018", "specific", "primary", "season2_start_date", "season2_end_date"), + action_specified("older_adults", "s3", "2018_2019", "specific", "primary", "season3_start_date", "season3_end_date"), + action_specified("older_adults", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_covid("older_adults", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_specified("older_adults", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_covid("older_adults", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_specified("older_adults", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_covid("older_adults", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_specified("older_adults", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + action_covid("older_adults", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Adults, Season: Codelist Type: Specific, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("adults", "s1", "2016_2017", "specific", "primary", "season1_start_date", "season1_end_date"), + action_specified("adults", "s2", "2017_2018", "specific", "primary", "season2_start_date", "season2_end_date"), + action_specified("adults", "s3", "2018_2019", "specific", "primary", "season3_start_date", "season3_end_date"), + action_specified("adults", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_covid("adults", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_specified("adults", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_covid("adults", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_specified("adults", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_covid("adults", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_specified("adults", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + action_covid("adults", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Children and Adolescents, Codelist Type: Specific, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("children_and_adolescents", "s1", "2016_2017", "specific", "primary", "season1_start_date", "season1_end_date"), + action_specified("children_and_adolescents", "s2", "2017_2018", "specific", "primary", "season2_start_date", "season2_end_date"), + action_specified("children_and_adolescents", "s3", "2018_2019", "specific", "primary", "season3_start_date", "season3_end_date"), + action_specified("children_and_adolescents", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_covid("children_and_adolescents", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_specified("children_and_adolescents", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_covid("children_and_adolescents", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_specified("children_and_adolescents", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_covid("children_and_adolescents", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_specified("children_and_adolescents", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + action_covid("children_and_adolescents", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Infants, Codelist Type: Specific, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("infants", "s1", "2016_2017", "specific", "primary", "season1_start_date", "season1_end_date"), + action_specified("infants", "s2", "2017_2018", "specific", "primary", "season2_start_date", "season2_end_date"), + action_specified("infants", "s3", "2018_2019", "specific", "primary", "season3_start_date", "season3_end_date"), + action_specified("infants", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_covid("infants", "s4", "2019_2020", "specific", "primary", "season4_start_date", "season4_end_date"), + action_specified("infants", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_covid("infants", "s5", "2020_2021", "specific", "primary", "season5_start_date", "season5_end_date"), + action_specified("infants", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_covid("infants", "s6", "2021_2022", "specific", "primary", "season6_start_date", "season6_end_date"), + action_specified("infants", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + action_covid("infants", "s7", "2022_2023", "specific", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "SENSITIVITY ANALYSES", "# # # # # # # # # # # # # # # # # # #"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults, Codelist Type: Sensitive, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("older_adults", "s1", "2016_2017", "sensitive", "primary", "season1_start_date", "season1_end_date"), + action_specified("older_adults", "s2", "2017_2018", "sensitive", "primary", "season2_start_date", "season2_end_date"), + action_specified("older_adults", "s3", "2018_2019", "sensitive", "primary", "season3_start_date", "season3_end_date"), + action_specified("older_adults", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_covid("older_adults", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_specified("older_adults", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_covid("older_adults", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_specified("older_adults", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_covid("older_adults", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_specified("older_adults", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + action_covid("older_adults", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Adults, Codelist Type: Sensitive, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("adults", "s1", "2016_2017", "sensitive", "primary", "season1_start_date", "season1_end_date"), + action_specified("adults", "s2", "2017_2018", "sensitive", "primary", "season2_start_date", "season2_end_date"), + action_specified("adults", "s3", "2018_2019", "sensitive", "primary", "season3_start_date", "season3_end_date"), + action_specified("adults", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_covid("adults", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_specified("adults", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_covid("adults", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_specified("adults", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_covid("adults", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_specified("adults", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + action_covid("adults", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Children and Adolescents, Codelist Type: Sensitive, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("children_and_adolescents", "s1", "2016_2017", "sensitive", "primary", "season1_start_date", "season1_end_date"), + action_specified("children_and_adolescents", "s2", "2017_2018", "sensitive", "primary", "season2_start_date", "season2_end_date"), + action_specified("children_and_adolescents", "s3", "2018_2019", "sensitive", "primary", "season3_start_date", "season3_end_date"), + action_specified("children_and_adolescents", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_covid("children_and_adolescents", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_specified("children_and_adolescents", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_covid("children_and_adolescents", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_specified("children_and_adolescents", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_covid("children_and_adolescents", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_specified("children_and_adolescents", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + action_covid("children_and_adolescents", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Infants, Codelist Type: Sensitive, Investigation Type: Primary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("infants", "s1", "2016_2017", "sensitive", "primary", "season1_start_date", "season1_end_date"), + action_specified("infants", "s2", "2017_2018", "sensitive", "primary", "season2_start_date", "season2_end_date"), + action_specified("infants", "s3", "2018_2019", "sensitive", "primary", "season3_start_date", "season3_end_date"), + action_specified("infants", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_covid("infants", "s4", "2019_2020", "sensitive", "primary", "season4_start_date", "season4_end_date"), + action_specified("infants", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_covid("infants", "s5", "2020_2021", "sensitive", "primary", "season5_start_date", "season5_end_date"), + action_specified("infants", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_covid("infants", "s6", "2021_2022", "sensitive", "primary", "season6_start_date", "season6_end_date"), + action_specified("infants", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + action_covid("infants", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "SECONDARY ANALYSES", "# # # # # # # # # # # # # # # # # # #"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults, Codelist Type: Sensitive, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("older_adults", "s1", "2016_2017", "sensitive", "secondary", "season1_start_date", "season1_end_date"), + action_specified("older_adults", "s2", "2017_2018", "sensitive", "secondary", "season2_start_date", "season2_end_date"), + action_specified("older_adults", "s3", "2018_2019", "sensitive", "secondary", "season3_start_date", "season3_end_date"), + action_specified("older_adults", "s4", "2019_2020", "sensitive", "secondary", "season4_start_date", "season4_end_date"), + action_specified("older_adults", "s5", "2020_2021", "sensitive", "secondary", "season5_start_date", "season5_end_date"), + action_specified("older_adults", "s6", "2021_2022", "sensitive", "secondary", "season6_start_date", "season6_end_date"), + action_specified("older_adults", "s7", "2022_2023", "sensitive", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Adults, Codelist Type: Sensitive, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("adults", "s1", "2016_2017", "sensitive", "secondary", "season1_start_date", "season1_end_date"), + action_specified("adults", "s2", "2017_2018", "sensitive", "secondary", "season2_start_date", "season2_end_date"), + action_specified("adults", "s3", "2018_2019", "sensitive", "secondary", "season3_start_date", "season3_end_date"), + action_specified("adults", "s4", "2019_2020", "sensitive", "secondary", "season4_start_date", "season4_end_date"), + action_specified("adults", "s5", "2020_2021", "sensitive", "secondary", "season5_start_date", "season5_end_date"), + action_specified("adults", "s6", "2021_2022", "sensitive", "secondary", "season6_start_date", "season6_end_date"), + action_specified("adults", "s7", "2022_2023", "sensitive", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Children and Adolescents, Codelist Type: Sensitive, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("children_and_adolescents", "s1", "2016_2017", "sensitive", "secondary", "season1_start_date", "season1_end_date"), + action_specified("children_and_adolescents", "s2", "2017_2018", "sensitive", "secondary", "season2_start_date", "season2_end_date"), + action_specified("children_and_adolescents", "s3", "2018_2019", "sensitive", "secondary", "season3_start_date", "season3_end_date"), + action_specified("children_and_adolescents", "s4", "2019_2020", "sensitive", "secondary", "season4_start_date", "season4_end_date"), + action_specified("children_and_adolescents", "s5", "2020_2021", "sensitive", "secondary", "season5_start_date", "season5_end_date"), + action_specified("children_and_adolescents", "s6", "2021_2022", "sensitive", "secondary", "season6_start_date", "season6_end_date"), + action_specified("children_and_adolescents", "s7", "2022_2023", "sensitive", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Infants, Codelist Type: Sensitive, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_specified("infants", "s1", "2016_2017", "sensitive", "secondary", "season1_start_date", "season1_end_date"), + action_specified("infants", "s2", "2017_2018", "sensitive", "secondary", "season2_start_date", "season2_end_date"), + action_specified("infants", "s3", "2018_2019", "sensitive", "secondary", "season3_start_date", "season3_end_date"), + action_specified("infants", "s4", "2019_2020", "sensitive", "secondary", "season4_start_date", "season4_end_date"), + action_specified("infants", "s5", "2020_2021", "sensitive", "secondary", "season5_start_date", "season5_end_date"), + action_specified("infants", "s6", "2021_2022", "sensitive", "secondary", "season6_start_date", "season6_end_date"), + action_specified("infants", "s7", "2022_2023", "sensitive", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "DESCRIPTIVE ANALYSES", "# # # # # # # # # # # # # # # # # # #"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults", "# # # # # # # # # # # # # # # # # # #"), + + action_descriptive("older_adults", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), + action_descriptive("older_adults", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_descriptive("older_adults", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_descriptive("older_adults", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), + action_descriptive("older_adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + action_descriptive("older_adults", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), + action_descriptive("older_adults", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Adults", "# # # # # # # # # # # # # # # # # # #"), + + action_descriptive("adults", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), + action_descriptive("adults", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_descriptive("adults", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_descriptive("adults", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), + action_descriptive("adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + action_descriptive("adults", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), + action_descriptive("adults", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Children and Adolescents", "# # # # # # # # # # # # # # # # # # #"), + + action_descriptive("children_and_adolescents", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), + action_descriptive("children_and_adolescents", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_descriptive("children_and_adolescents", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_descriptive("children_and_adolescents", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), + action_descriptive("children_and_adolescents", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + action_descriptive("children_and_adolescents", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), + action_descriptive("children_and_adolescents", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Infants", "# # # # # # # # # # # # # # # # # # #"), + + action_descriptive("infants", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), + action_descriptive("infants", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_descriptive("infants", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_descriptive("infants", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), + action_descriptive("infants", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + action_descriptive("infants", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), + action_descriptive("infants", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Files for release", "# # # # # # # # # # # # # # # # # # #"), + + action_finalise("older_adults"), + action_finalise("adults"), + action_finalise("children_and_adolescents"), + action_finalise("infants"), + + # action( + # name = "release_objects", + # run = "r:latest analysis/release_objects.R", + # needs = list( + # "combine_age75plus_descriptives", + # "combine_age75plus_contrasts", + # "combine_cv_descriptives", + # "combine_cv_contrasts" + # ), + # moderately_sensitive = lst( + # releaselist = "output/files-for-release.txt", + # command = "output/osrelease-command.txt", + # output1 = "output/release-objects/*.csv", + # output2 = "output/release-objects/*/*.csv", + # ) + # ), + + comment("# # # # # # # # # # # # # # # # # # #", "End", "# # # # # # # # # # # # # # # # # # #") + +) + + +project_list <- splice( + defaults_list, + list(actions = actions_list) +) + +## convert list to yaml, reformat comments and whitespace ---- +thisproject <- as.yaml(project_list, indent=2) %>% + # convert comment actions to comments + convert_comment_actions() %>% + # add one blank line before level 1 and level 2 keys + str_replace_all("\\\n(\\w)", "\n\n\\1") %>% + str_replace_all("\\\n\\s\\s(\\w)", "\n\n \\1") + + +# if running via opensafely, check that the project on disk is the same as the project created here: +if (Sys.getenv("OPENSAFELY_BACKEND") %in% c("expectations", "tpp")){ + + thisprojectsplit <- str_split(thisproject, "\n")[[1]] + currentproject <- readLines(here("project.yaml")) + + stopifnot("project.yaml is not up-to-date with create-project.R. Run create-project.R before running further actions." = identical(thisprojectsplit, currentproject)) + +# if running manually, output new project as normal +} else if (Sys.getenv("OPENSAFELY_BACKEND") %in% c("")){ + +## output to file ---- + writeLines(thisproject, here("project.yaml")) +#yaml::write_yaml(project_list, file =here("project.yaml")) + +## grab all action names and send to a txt file + +names(actions_list) %>% tibble(action=.) %>% + mutate( + model = action=="" & lag(action!="", 1, TRUE), + model_number = cumsum(model), + ) %>% + group_by(model_number) %>% + summarise( + sets = str_trim(paste(action, collapse=" ")) + ) %>% pull(sets) %>% + paste(collapse="\n") %>% + writeLines(here("actions.txt")) + +# fail if backend not recognised +} else { + stop("Backend not recognised") +} + + diff --git a/project.yaml b/project.yaml index bf58537..9b36af8 100644 --- a/project.yaml +++ b/project.yaml @@ -1,787 +1,45347 @@ version: '3.0' -# Ignore this`expectation` block. It is required but not used, and will be removed in future versions. expectations: + population_size: 100000 actions: -### exploratory analysis - -## season 1 (2016/17) - cohort inclusion + ## # # # # # # # # # # # # # # # # # # # + ## DO NOT EDIT project.yaml DIRECTLY + ## This file is created by create-project.R + ## Edit and run create-project.R to update the project.yaml + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Pre-server scripts + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Inclusion/Exclusion Flow Chart Actions: Older Adults + ## # # # # # # # # # # # # # # # # # # # generate_flow_chart_data_older_adults_s1: - run: > + run: |- ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py --output output/flow_chart/older_adults_2016_2017_flow_chart.csv --dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow - -- older_adults season1_start_date season1_end_date + -- older_adults season1_start_date season1_end_date older_adults s1 2016_2017 season1_start_date season1_end_date outputs: highly_sensitive: dataset: output/flow_chart/older_adults_2016_2017_flow_chart.csv - - process_flow_chart_older_adults_s1: - run: r:latest analysis/cohort_criteria.R older_adults season1_start_date season1_end_date - needs: [generate_flow_chart_data_older_adults_s1] + + process_flow_chart_data_older_adults_s1: + run: r:latest analysis/cohort_criteria.R older_adults season1_start_date season1_end_date + older_adults s1 2016_2017 season1_start_date season1_end_date + needs: + - generate_flow_chart_data_older_adults_s1 outputs: highly_sensitive: cohort: output/flow_chart/flow_chart_processed_older_adults_2016_2017.csv + generate_flow_chart_data_older_adults_s2: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/older_adults_2017_2018_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2017_2018.arrow + -- older_adults season2_start_date season2_end_date older_adults s2 2017_2018 season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/older_adults_2017_2018_flow_chart.csv + + process_flow_chart_data_older_adults_s2: + run: r:latest analysis/cohort_criteria.R older_adults season2_start_date season2_end_date + older_adults s2 2017_2018 season2_start_date season2_end_date + needs: + - generate_flow_chart_data_older_adults_s2 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_older_adults_2017_2018.csv + + generate_flow_chart_data_older_adults_s3: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/older_adults_2018_2019_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2018_2019.arrow + -- older_adults season3_start_date season3_end_date older_adults s3 2018_2019 season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/older_adults_2018_2019_flow_chart.csv + + process_flow_chart_data_older_adults_s3: + run: r:latest analysis/cohort_criteria.R older_adults season3_start_date season3_end_date + older_adults s3 2018_2019 season3_start_date season3_end_date + needs: + - generate_flow_chart_data_older_adults_s3 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_older_adults_2018_2019.csv + + generate_flow_chart_data_older_adults_s4: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/older_adults_2019_2020_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2019_2020.arrow + -- older_adults season4_start_date season4_end_date older_adults s4 2019_2020 season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/older_adults_2019_2020_flow_chart.csv + + process_flow_chart_data_older_adults_s4: + run: r:latest analysis/cohort_criteria.R older_adults season4_start_date season4_end_date + older_adults s4 2019_2020 season4_start_date season4_end_date + needs: + - generate_flow_chart_data_older_adults_s4 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_older_adults_2019_2020.csv + + generate_flow_chart_data_older_adults_s5: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/older_adults_2020_2021_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2020_2021.arrow + -- older_adults season5_start_date season5_end_date older_adults s5 2020_2021 season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/older_adults_2020_2021_flow_chart.csv + + process_flow_chart_data_older_adults_s5: + run: r:latest analysis/cohort_criteria.R older_adults season5_start_date season5_end_date + older_adults s5 2020_2021 season5_start_date season5_end_date + needs: + - generate_flow_chart_data_older_adults_s5 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_older_adults_2020_2021.csv + + generate_flow_chart_data_older_adults_s6: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/older_adults_2021_2022_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2021_2022.arrow + -- older_adults season6_start_date season6_end_date older_adults s6 2021_2022 season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/older_adults_2021_2022_flow_chart.csv + + process_flow_chart_data_older_adults_s6: + run: r:latest analysis/cohort_criteria.R older_adults season6_start_date season6_end_date + older_adults s6 2021_2022 season6_start_date season6_end_date + needs: + - generate_flow_chart_data_older_adults_s6 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_older_adults_2021_2022.csv + + generate_flow_chart_data_older_adults_s7: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/older_adults_2022_2023_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2022_2023.arrow + -- older_adults season7_start_date season7_end_date older_adults s7 2022_2023 season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/older_adults_2022_2023_flow_chart.csv + + process_flow_chart_data_older_adults_s7: + run: r:latest analysis/cohort_criteria.R older_adults season7_start_date season7_end_date + older_adults s7 2022_2023 season7_start_date season7_end_date + needs: + - generate_flow_chart_data_older_adults_s7 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_older_adults_2022_2023.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Inclusion/Exclusion Flow Chart Actions: Adults + ## # # # # # # # # # # # # # # # # # # # + generate_flow_chart_data_adults_s1: - run: > + run: |- ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py --output output/flow_chart/adults_2016_2017_flow_chart.csv --dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow - -- adults season1_start_date season1_end_date + -- adults season1_start_date season1_end_date adults s1 2016_2017 season1_start_date season1_end_date outputs: highly_sensitive: dataset: output/flow_chart/adults_2016_2017_flow_chart.csv - process_flow_chart_adults_s1: - run: r:latest analysis/cohort_criteria.R adults season1_start_date season1_end_date - needs: [generate_flow_chart_data_adults_s1] + process_flow_chart_data_adults_s1: + run: r:latest analysis/cohort_criteria.R adults season1_start_date season1_end_date + adults s1 2016_2017 season1_start_date season1_end_date + needs: + - generate_flow_chart_data_adults_s1 outputs: highly_sensitive: cohort: output/flow_chart/flow_chart_processed_adults_2016_2017.csv - generate_flow_chart_data_children_and_adolescents_s1: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py - --output output/flow_chart/children_and_adolescents_2016_2017_flow_chart.csv - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow - -- children_and_adolescents season1_start_date season1_end_date + generate_flow_chart_data_adults_s2: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/adults_2017_2018_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_adults_2017_2018.arrow + -- adults season2_start_date season2_end_date adults s2 2017_2018 season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/adults_2017_2018_flow_chart.csv + + process_flow_chart_data_adults_s2: + run: r:latest analysis/cohort_criteria.R adults season2_start_date season2_end_date + adults s2 2017_2018 season2_start_date season2_end_date + needs: + - generate_flow_chart_data_adults_s2 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_adults_2017_2018.csv + + generate_flow_chart_data_adults_s3: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/adults_2018_2019_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_adults_2018_2019.arrow + -- adults season3_start_date season3_end_date adults s3 2018_2019 season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/adults_2018_2019_flow_chart.csv + + process_flow_chart_data_adults_s3: + run: r:latest analysis/cohort_criteria.R adults season3_start_date season3_end_date + adults s3 2018_2019 season3_start_date season3_end_date + needs: + - generate_flow_chart_data_adults_s3 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_adults_2018_2019.csv + + generate_flow_chart_data_adults_s4: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/adults_2019_2020_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_adults_2019_2020.arrow + -- adults season4_start_date season4_end_date adults s4 2019_2020 season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/adults_2019_2020_flow_chart.csv + + process_flow_chart_data_adults_s4: + run: r:latest analysis/cohort_criteria.R adults season4_start_date season4_end_date + adults s4 2019_2020 season4_start_date season4_end_date + needs: + - generate_flow_chart_data_adults_s4 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_adults_2019_2020.csv + + generate_flow_chart_data_adults_s5: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/adults_2020_2021_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_adults_2020_2021.arrow + -- adults season5_start_date season5_end_date adults s5 2020_2021 season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/adults_2020_2021_flow_chart.csv + + process_flow_chart_data_adults_s5: + run: r:latest analysis/cohort_criteria.R adults season5_start_date season5_end_date + adults s5 2020_2021 season5_start_date season5_end_date + needs: + - generate_flow_chart_data_adults_s5 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_adults_2020_2021.csv + + generate_flow_chart_data_adults_s6: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/adults_2021_2022_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_adults_2021_2022.arrow + -- adults season6_start_date season6_end_date adults s6 2021_2022 season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/adults_2021_2022_flow_chart.csv + + process_flow_chart_data_adults_s6: + run: r:latest analysis/cohort_criteria.R adults season6_start_date season6_end_date + adults s6 2021_2022 season6_start_date season6_end_date + needs: + - generate_flow_chart_data_adults_s6 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_adults_2021_2022.csv + + generate_flow_chart_data_adults_s7: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/adults_2022_2023_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow + -- adults season7_start_date season7_end_date adults s7 2022_2023 season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/adults_2022_2023_flow_chart.csv + + process_flow_chart_data_adults_s7: + run: r:latest analysis/cohort_criteria.R adults season7_start_date season7_end_date + adults s7 2022_2023 season7_start_date season7_end_date + needs: + - generate_flow_chart_data_adults_s7 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_adults_2022_2023.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Inclusion/Exclusion Flow Chart Actions: Children and Adolescents + ## # # # # # # # # # # # # # # # # # # # + + generate_flow_chart_data_children_and_adolescents_s1: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/children_and_adolescents_2016_2017_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow + -- children_and_adolescents season1_start_date season1_end_date children_and_adolescents s1 2016_2017 season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/children_and_adolescents_2016_2017_flow_chart.csv + + process_flow_chart_data_children_and_adolescents_s1: + run: r:latest analysis/cohort_criteria.R children_and_adolescents season1_start_date + season1_end_date children_and_adolescents s1 2016_2017 season1_start_date season1_end_date + needs: + - generate_flow_chart_data_children_and_adolescents_s1 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2016_2017.csv + + generate_flow_chart_data_children_and_adolescents_s2: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/children_and_adolescents_2017_2018_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2017_2018.arrow + -- children_and_adolescents season2_start_date season2_end_date children_and_adolescents s2 2017_2018 season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/children_and_adolescents_2017_2018_flow_chart.csv + + process_flow_chart_data_children_and_adolescents_s2: + run: r:latest analysis/cohort_criteria.R children_and_adolescents season2_start_date + season2_end_date children_and_adolescents s2 2017_2018 season2_start_date season2_end_date + needs: + - generate_flow_chart_data_children_and_adolescents_s2 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2017_2018.csv + + generate_flow_chart_data_children_and_adolescents_s3: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/children_and_adolescents_2018_2019_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2018_2019.arrow + -- children_and_adolescents season3_start_date season3_end_date children_and_adolescents s3 2018_2019 season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/children_and_adolescents_2018_2019_flow_chart.csv + + process_flow_chart_data_children_and_adolescents_s3: + run: r:latest analysis/cohort_criteria.R children_and_adolescents season3_start_date + season3_end_date children_and_adolescents s3 2018_2019 season3_start_date season3_end_date + needs: + - generate_flow_chart_data_children_and_adolescents_s3 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2018_2019.csv + + generate_flow_chart_data_children_and_adolescents_s4: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/children_and_adolescents_2019_2020_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2019_2020.arrow + -- children_and_adolescents season4_start_date season4_end_date children_and_adolescents s4 2019_2020 season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/children_and_adolescents_2019_2020_flow_chart.csv + + process_flow_chart_data_children_and_adolescents_s4: + run: r:latest analysis/cohort_criteria.R children_and_adolescents season4_start_date + season4_end_date children_and_adolescents s4 2019_2020 season4_start_date season4_end_date + needs: + - generate_flow_chart_data_children_and_adolescents_s4 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2019_2020.csv + + generate_flow_chart_data_children_and_adolescents_s5: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/children_and_adolescents_2020_2021_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2020_2021.arrow + -- children_and_adolescents season5_start_date season5_end_date children_and_adolescents s5 2020_2021 season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/children_and_adolescents_2020_2021_flow_chart.csv + + process_flow_chart_data_children_and_adolescents_s5: + run: r:latest analysis/cohort_criteria.R children_and_adolescents season5_start_date + season5_end_date children_and_adolescents s5 2020_2021 season5_start_date season5_end_date + needs: + - generate_flow_chart_data_children_and_adolescents_s5 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2020_2021.csv + + generate_flow_chart_data_children_and_adolescents_s6: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/children_and_adolescents_2021_2022_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2021_2022.arrow + -- children_and_adolescents season6_start_date season6_end_date children_and_adolescents s6 2021_2022 season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/children_and_adolescents_2021_2022_flow_chart.csv + + process_flow_chart_data_children_and_adolescents_s6: + run: r:latest analysis/cohort_criteria.R children_and_adolescents season6_start_date + season6_end_date children_and_adolescents s6 2021_2022 season6_start_date season6_end_date + needs: + - generate_flow_chart_data_children_and_adolescents_s6 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2021_2022.csv + + generate_flow_chart_data_children_and_adolescents_s7: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/children_and_adolescents_2022_2023_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow + -- children_and_adolescents season7_start_date season7_end_date children_and_adolescents s7 2022_2023 season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/children_and_adolescents_2022_2023_flow_chart.csv + + process_flow_chart_data_children_and_adolescents_s7: + run: r:latest analysis/cohort_criteria.R children_and_adolescents season7_start_date + season7_end_date children_and_adolescents s7 2022_2023 season7_start_date season7_end_date + needs: + - generate_flow_chart_data_children_and_adolescents_s7 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2022_2023.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Inclusion/Exclusion Flow Chart Actions: Infants + ## # # # # # # # # # # # # # # # # # # # + + generate_flow_chart_data_infants_s1: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/infants_2016_2017_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow + -- infants season1_start_date season1_end_date infants s1 2016_2017 season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/infants_2016_2017_flow_chart.csv + + process_flow_chart_data_infants_s1: + run: r:latest analysis/cohort_criteria.R infants season1_start_date season1_end_date + infants s1 2016_2017 season1_start_date season1_end_date + needs: + - generate_flow_chart_data_infants_s1 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_infants_2016_2017.csv + + generate_flow_chart_data_infants_s2: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/infants_2017_2018_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow + -- infants season2_start_date season2_end_date infants s2 2017_2018 season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/infants_2017_2018_flow_chart.csv + + process_flow_chart_data_infants_s2: + run: r:latest analysis/cohort_criteria.R infants season2_start_date season2_end_date + infants s2 2017_2018 season2_start_date season2_end_date + needs: + - generate_flow_chart_data_infants_s2 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_infants_2017_2018.csv + + generate_flow_chart_data_infants_s3: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/infants_2018_2019_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow + -- infants season3_start_date season3_end_date infants s3 2018_2019 season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/infants_2018_2019_flow_chart.csv + + process_flow_chart_data_infants_s3: + run: r:latest analysis/cohort_criteria.R infants season3_start_date season3_end_date + infants s3 2018_2019 season3_start_date season3_end_date + needs: + - generate_flow_chart_data_infants_s3 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_infants_2018_2019.csv + + generate_flow_chart_data_infants_s4: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/infants_2019_2020_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow + -- infants season4_start_date season4_end_date infants s4 2019_2020 season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/infants_2019_2020_flow_chart.csv + + process_flow_chart_data_infants_s4: + run: r:latest analysis/cohort_criteria.R infants season4_start_date season4_end_date + infants s4 2019_2020 season4_start_date season4_end_date + needs: + - generate_flow_chart_data_infants_s4 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_infants_2019_2020.csv + + generate_flow_chart_data_infants_s5: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/infants_2020_2021_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow + -- infants season5_start_date season5_end_date infants s5 2020_2021 season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/infants_2020_2021_flow_chart.csv + + process_flow_chart_data_infants_s5: + run: r:latest analysis/cohort_criteria.R infants season5_start_date season5_end_date + infants s5 2020_2021 season5_start_date season5_end_date + needs: + - generate_flow_chart_data_infants_s5 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_infants_2020_2021.csv + + generate_flow_chart_data_infants_s6: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/infants_2021_2022_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_infants_2021_2022.arrow + -- infants season6_start_date season6_end_date infants s6 2021_2022 season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/infants_2021_2022_flow_chart.csv + + process_flow_chart_data_infants_s6: + run: r:latest analysis/cohort_criteria.R infants season6_start_date season6_end_date + infants s6 2021_2022 season6_start_date season6_end_date + needs: + - generate_flow_chart_data_infants_s6 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_infants_2021_2022.csv + + generate_flow_chart_data_infants_s7: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py + --output output/flow_chart/infants_2022_2023_flow_chart.csv + --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow + -- infants season7_start_date season7_end_date infants s7 2022_2023 season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/flow_chart/infants_2022_2023_flow_chart.csv + + process_flow_chart_data_infants_s7: + run: r:latest analysis/cohort_criteria.R infants season7_start_date season7_end_date + infants s7 2022_2023 season7_start_date season7_end_date + needs: + - generate_flow_chart_data_infants_s7 + outputs: + highly_sensitive: + cohort: output/flow_chart/flow_chart_processed_infants_2022_2023.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Household Information Actions + ## # # # # # # # # # # # # # # # # # # # + + extract_household_information_s1: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_2016_2017.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_2016_2017.arrow + -- season1_start_date season1_end_date s1 2016_2017 season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_household_2016_2017.arrow + + process_household_information_s1: + run: r:latest analysis/data_processing_household.R season1_start_date season1_end_date + s1 2016_2017 season1_start_date season1_end_date + needs: + - extract_household_information_s1 + outputs: + highly_sensitive: + arrow: output/data/input_household_processed_2016_2017.arrow + + extract_household_information_s2: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_2017_2018.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_2017_2018.arrow + -- season2_start_date season2_end_date s2 2017_2018 season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_household_2017_2018.arrow + + process_household_information_s2: + run: r:latest analysis/data_processing_household.R season2_start_date season2_end_date + s2 2017_2018 season2_start_date season2_end_date + needs: + - extract_household_information_s2 + outputs: + highly_sensitive: + arrow: output/data/input_household_processed_2017_2018.arrow + + extract_household_information_s3: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_2018_2019.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_2018_2019.arrow + -- season3_start_date season3_end_date s3 2018_2019 season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_household_2018_2019.arrow + + process_household_information_s3: + run: r:latest analysis/data_processing_household.R season3_start_date season3_end_date + s3 2018_2019 season3_start_date season3_end_date + needs: + - extract_household_information_s3 + outputs: + highly_sensitive: + arrow: output/data/input_household_processed_2018_2019.arrow + + extract_household_information_s4: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_2019_2020.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_2019_2020.arrow + -- season4_start_date season4_end_date s4 2019_2020 season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_household_2019_2020.arrow + + process_household_information_s4: + run: r:latest analysis/data_processing_household.R season4_start_date season4_end_date + s4 2019_2020 season4_start_date season4_end_date + needs: + - extract_household_information_s4 + outputs: + highly_sensitive: + arrow: output/data/input_household_processed_2019_2020.arrow + + extract_household_information_s5: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_2020_2021.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_2020_2021.arrow + -- season5_start_date season5_end_date s5 2020_2021 season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_household_2020_2021.arrow + + process_household_information_s5: + run: r:latest analysis/data_processing_household.R season5_start_date season5_end_date + s5 2020_2021 season5_start_date season5_end_date + needs: + - extract_household_information_s5 + outputs: + highly_sensitive: + arrow: output/data/input_household_processed_2020_2021.arrow + + extract_household_information_s6: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_2021_2022.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_2021_2022.arrow + -- season6_start_date season6_end_date s6 2021_2022 season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_household_2021_2022.arrow + + process_household_information_s6: + run: r:latest analysis/data_processing_household.R season6_start_date season6_end_date + s6 2021_2022 season6_start_date season6_end_date + needs: + - extract_household_information_s6 + outputs: + highly_sensitive: + arrow: output/data/input_household_processed_2021_2022.arrow + + extract_household_information_s7: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition_household.py + --output output/data/input_household_2022_2023.arrow + --dummy-data-file analysis/dummydata/dummyextract_household_2022_2023.arrow + -- season7_start_date season7_end_date s7 2022_2023 season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_household_2022_2023.arrow + + process_household_information_s7: + run: r:latest analysis/data_processing_household.R season7_start_date season7_end_date + s7 2022_2023 season7_start_date season7_end_date + needs: + - extract_household_information_s7 + outputs: + highly_sensitive: + arrow: output/data/input_household_processed_2022_2023.arrow + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults, Codelist Type: Specific, Investigation Type: Primary + + + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_older_adults_s1_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2016_2017_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow + -- older_adults season1_start_date season1_end_date specific primary older_adults s1 2016_2017 specific primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2016_2017_specific_primary.arrow + + process_dataset_older_adults_s1_specific_primary: + run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date + specific primary older_adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - generate_dataset_older_adults_s1_specific_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2016_2017_specific_primary.arrow + + describe_dataset_older_adults_s1_specific_primary: + run: r:latest analysis/report.R older_adults season1_start_date season1_end_date + specific primary older_adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season1_start_date season1_end_date specific primary older_adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season1_start_date + season1_end_date specific primary older_adults s1 2016_2017 specific primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2016_2017_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season1_start_date season1_end_date specific primary older_adults + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2016_2017_specific_primary.csv + + generate_dataset_older_adults_s2_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2017_2018_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2017_2018.arrow + -- older_adults season2_start_date season2_end_date specific primary older_adults s2 2017_2018 specific primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2017_2018_specific_primary.arrow + + process_dataset_older_adults_s2_specific_primary: + run: r:latest analysis/data_processing.R older_adults season2_start_date season2_end_date + specific primary older_adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - generate_dataset_older_adults_s2_specific_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2017_2018_specific_primary.arrow + + describe_dataset_older_adults_s2_specific_primary: + run: r:latest analysis/report.R older_adults season2_start_date season2_end_date + specific primary older_adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season2_start_date season2_end_date specific primary older_adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season2_start_date + season2_end_date specific primary older_adults s2 2017_2018 specific primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2017_2018_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season2_start_date season2_end_date specific primary older_adults + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2017_2018_specific_primary.csv + + generate_dataset_older_adults_s3_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2018_2019_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2018_2019.arrow + -- older_adults season3_start_date season3_end_date specific primary older_adults s3 2018_2019 specific primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2018_2019_specific_primary.arrow + + process_dataset_older_adults_s3_specific_primary: + run: r:latest analysis/data_processing.R older_adults season3_start_date season3_end_date + specific primary older_adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - generate_dataset_older_adults_s3_specific_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2018_2019_specific_primary.arrow + + describe_dataset_older_adults_s3_specific_primary: + run: r:latest analysis/report.R older_adults season3_start_date season3_end_date + specific primary older_adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season3_start_date season3_end_date specific primary older_adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season3_start_date + season3_end_date specific primary older_adults s3 2018_2019 specific primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2018_2019_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season3_start_date season3_end_date specific primary older_adults + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2018_2019_specific_primary.csv + + generate_dataset_older_adults_s4_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2019_2020_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2019_2020.arrow + -- older_adults season4_start_date season4_end_date specific primary older_adults s4 2019_2020 specific primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2019_2020_specific_primary.arrow + + process_dataset_older_adults_s4_specific_primary: + run: r:latest analysis/data_processing.R older_adults season4_start_date season4_end_date + specific primary older_adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - generate_dataset_older_adults_s4_specific_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2019_2020_specific_primary.arrow + + describe_dataset_older_adults_s4_specific_primary: + run: r:latest analysis/report.R older_adults season4_start_date season4_end_date + specific primary older_adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season4_start_date + season4_end_date specific primary older_adults s4 2019_2020 specific primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date specific primary older_adults + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2019_2020_specific_primary.csv + + analyse_dataset_older_adults_further_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season4_start_date season4_end_date specific primary older_adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2019_2020_specific_primary.csv + + generate_dataset_older_adults_s5_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2020_2021_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2020_2021.arrow + -- older_adults season5_start_date season5_end_date specific primary older_adults s5 2020_2021 specific primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2020_2021_specific_primary.arrow + + process_dataset_older_adults_s5_specific_primary: + run: r:latest analysis/data_processing.R older_adults season5_start_date season5_end_date + specific primary older_adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - generate_dataset_older_adults_s5_specific_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2020_2021_specific_primary.arrow + + describe_dataset_older_adults_s5_specific_primary: + run: r:latest analysis/report.R older_adults season5_start_date season5_end_date + specific primary older_adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season5_start_date + season5_end_date specific primary older_adults s5 2020_2021 specific primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date specific primary older_adults + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2020_2021_specific_primary.csv + + analyse_dataset_older_adults_further_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season5_start_date season5_end_date specific primary older_adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2020_2021_specific_primary.csv + + generate_dataset_older_adults_s6_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2021_2022_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2021_2022.arrow + -- older_adults season6_start_date season6_end_date specific primary older_adults s6 2021_2022 specific primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2021_2022_specific_primary.arrow + + process_dataset_older_adults_s6_specific_primary: + run: r:latest analysis/data_processing.R older_adults season6_start_date season6_end_date + specific primary older_adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - generate_dataset_older_adults_s6_specific_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2021_2022_specific_primary.arrow + + describe_dataset_older_adults_s6_specific_primary: + run: r:latest analysis/report.R older_adults season6_start_date season6_end_date + specific primary older_adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season6_start_date + season6_end_date specific primary older_adults s6 2021_2022 specific primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date specific primary older_adults + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2021_2022_specific_primary.csv + + analyse_dataset_older_adults_further_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season6_start_date season6_end_date specific primary older_adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2021_2022_specific_primary.csv + + generate_dataset_older_adults_s7_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2022_2023_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2022_2023.arrow + -- older_adults season7_start_date season7_end_date specific primary older_adults s7 2022_2023 specific primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2022_2023_specific_primary.arrow + + process_dataset_older_adults_s7_specific_primary: + run: r:latest analysis/data_processing.R older_adults season7_start_date season7_end_date + specific primary older_adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - generate_dataset_older_adults_s7_specific_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2022_2023_specific_primary.arrow + + describe_dataset_older_adults_s7_specific_primary: + run: r:latest analysis/report.R older_adults season7_start_date season7_end_date + specific primary older_adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season7_start_date + season7_end_date specific primary older_adults s7 2022_2023 specific primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date specific primary older_adults + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2022_2023_specific_primary.csv + + analyse_dataset_older_adults_further_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season7_start_date season7_end_date specific primary older_adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2022_2023_specific_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Adults, Season: Codelist Type: Specific, Investigation Type: Primary + + + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_adults_s1_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2016_2017_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow + -- adults season1_start_date season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2016_2017_specific_primary.arrow + + process_dataset_adults_s1_specific_primary: + run: r:latest analysis/data_processing.R adults season1_start_date season1_end_date + specific primary adults s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - generate_dataset_adults_s1_specific_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2016_2017_specific_primary.arrow + + describe_dataset_adults_s1_specific_primary: + run: r:latest analysis/report.R adults season1_start_date season1_end_date specific + primary adults s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season1_start_date season1_end_date specific primary adults s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season1_start_date season1_end_date specific primary adults s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season1_start_date season1_end_date specific primary adults s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season1_start_date season1_end_date specific primary adults s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season1_start_date + season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2016_2017_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season1_start_date season1_end_date specific primary adults s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2016_2017_specific_primary.csv + + generate_dataset_adults_s2_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2017_2018_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2017_2018.arrow + -- adults season2_start_date season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2017_2018_specific_primary.arrow + + process_dataset_adults_s2_specific_primary: + run: r:latest analysis/data_processing.R adults season2_start_date season2_end_date + specific primary adults s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - generate_dataset_adults_s2_specific_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2017_2018_specific_primary.arrow + + describe_dataset_adults_s2_specific_primary: + run: r:latest analysis/report.R adults season2_start_date season2_end_date specific + primary adults s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season2_start_date season2_end_date specific primary adults s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season2_start_date season2_end_date specific primary adults s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season2_start_date season2_end_date specific primary adults s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season2_start_date season2_end_date specific primary adults s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season2_start_date + season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2017_2018_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season2_start_date season2_end_date specific primary adults s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2017_2018_specific_primary.csv + + generate_dataset_adults_s3_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2018_2019_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2018_2019.arrow + -- adults season3_start_date season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2018_2019_specific_primary.arrow + + process_dataset_adults_s3_specific_primary: + run: r:latest analysis/data_processing.R adults season3_start_date season3_end_date + specific primary adults s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - generate_dataset_adults_s3_specific_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2018_2019_specific_primary.arrow + + describe_dataset_adults_s3_specific_primary: + run: r:latest analysis/report.R adults season3_start_date season3_end_date specific + primary adults s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season3_start_date season3_end_date specific primary adults s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season3_start_date season3_end_date specific primary adults s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season3_start_date season3_end_date specific primary adults s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season3_start_date season3_end_date specific primary adults s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season3_start_date + season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2018_2019_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season3_start_date season3_end_date specific primary adults s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2018_2019_specific_primary.csv + + generate_dataset_adults_s4_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2019_2020_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2019_2020.arrow + -- adults season4_start_date season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2019_2020_specific_primary.arrow + + process_dataset_adults_s4_specific_primary: + run: r:latest analysis/data_processing.R adults season4_start_date season4_end_date + specific primary adults s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - generate_dataset_adults_s4_specific_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2019_2020_specific_primary.arrow + + describe_dataset_adults_s4_specific_primary: + run: r:latest analysis/report.R adults season4_start_date season4_end_date specific + primary adults s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date specific primary adults s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season4_start_date season4_end_date specific primary adults s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2019_2020_specific_primary.csv + + analyse_dataset_adults_further_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season4_start_date + season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2019_2020_specific_primary.csv + + generate_dataset_adults_s5_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2020_2021_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2020_2021.arrow + -- adults season5_start_date season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2020_2021_specific_primary.arrow + + process_dataset_adults_s5_specific_primary: + run: r:latest analysis/data_processing.R adults season5_start_date season5_end_date + specific primary adults s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - generate_dataset_adults_s5_specific_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2020_2021_specific_primary.arrow + + describe_dataset_adults_s5_specific_primary: + run: r:latest analysis/report.R adults season5_start_date season5_end_date specific + primary adults s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date specific primary adults s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season5_start_date season5_end_date specific primary adults s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2020_2021_specific_primary.csv + + analyse_dataset_adults_further_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season5_start_date + season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2020_2021_specific_primary.csv + + generate_dataset_adults_s6_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2021_2022_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2021_2022.arrow + -- adults season6_start_date season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2021_2022_specific_primary.arrow + + process_dataset_adults_s6_specific_primary: + run: r:latest analysis/data_processing.R adults season6_start_date season6_end_date + specific primary adults s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - generate_dataset_adults_s6_specific_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2021_2022_specific_primary.arrow + + describe_dataset_adults_s6_specific_primary: + run: r:latest analysis/report.R adults season6_start_date season6_end_date specific + primary adults s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date specific primary adults s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season6_start_date season6_end_date specific primary adults s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2021_2022_specific_primary.csv + + analyse_dataset_adults_further_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season6_start_date + season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2021_2022_specific_primary.csv + + generate_dataset_adults_s7_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2022_2023_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow + -- adults season7_start_date season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2022_2023_specific_primary.arrow + + process_dataset_adults_s7_specific_primary: + run: r:latest analysis/data_processing.R adults season7_start_date season7_end_date + specific primary adults s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - generate_dataset_adults_s7_specific_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2022_2023_specific_primary.arrow + + describe_dataset_adults_s7_specific_primary: + run: r:latest analysis/report.R adults season7_start_date season7_end_date specific + primary adults s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date specific primary adults s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season7_start_date season7_end_date specific primary adults s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2022_2023_specific_primary.csv + + analyse_dataset_adults_further_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season7_start_date + season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2022_2023_specific_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Children and Adolescents, Codelist Type: Specific, Investigation + Type: Primary + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_children_and_adolescents_s1_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2016_2017_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow + -- children_and_adolescents season1_start_date season1_end_date specific primary children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2016_2017_specific_primary.arrow + + process_dataset_children_and_adolescents_s1_specific_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season1_start_date + season1_end_date specific primary children_and_adolescents s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - generate_dataset_children_and_adolescents_s1_specific_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2016_2017_specific_primary.arrow + + describe_dataset_children_and_adolescents_s1_specific_primary: + run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date + specific primary children_and_adolescents s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season1_start_date season1_end_date specific primary children_and_adolescents + s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season1_start_date season1_end_date specific primary + children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2016_2017_specific_primary.csv + + generate_dataset_children_and_adolescents_s2_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2017_2018_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2017_2018.arrow + -- children_and_adolescents season2_start_date season2_end_date specific primary children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2017_2018_specific_primary.arrow + + process_dataset_children_and_adolescents_s2_specific_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season2_start_date + season2_end_date specific primary children_and_adolescents s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - generate_dataset_children_and_adolescents_s2_specific_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2017_2018_specific_primary.arrow + + describe_dataset_children_and_adolescents_s2_specific_primary: + run: r:latest analysis/report.R children_and_adolescents season2_start_date season2_end_date + specific primary children_and_adolescents s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season2_start_date season2_end_date specific primary children_and_adolescents + s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season2_start_date season2_end_date specific primary + children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2017_2018_specific_primary.csv + + generate_dataset_children_and_adolescents_s3_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2018_2019_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2018_2019.arrow + -- children_and_adolescents season3_start_date season3_end_date specific primary children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2018_2019_specific_primary.arrow + + process_dataset_children_and_adolescents_s3_specific_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season3_start_date + season3_end_date specific primary children_and_adolescents s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - generate_dataset_children_and_adolescents_s3_specific_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2018_2019_specific_primary.arrow + + describe_dataset_children_and_adolescents_s3_specific_primary: + run: r:latest analysis/report.R children_and_adolescents season3_start_date season3_end_date + specific primary children_and_adolescents s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season3_start_date season3_end_date specific primary children_and_adolescents + s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season3_start_date season3_end_date specific primary + children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2018_2019_specific_primary.csv + + generate_dataset_children_and_adolescents_s4_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2019_2020_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2019_2020.arrow + -- children_and_adolescents season4_start_date season4_end_date specific primary children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2019_2020_specific_primary.arrow + + process_dataset_children_and_adolescents_s4_specific_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season4_start_date + season4_end_date specific primary children_and_adolescents s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - generate_dataset_children_and_adolescents_s4_specific_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2019_2020_specific_primary.arrow + + describe_dataset_children_and_adolescents_s4_specific_primary: + run: r:latest analysis/report.R children_and_adolescents season4_start_date season4_end_date + specific primary children_and_adolescents s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date specific primary + children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season4_start_date season4_end_date specific primary children_and_adolescents + s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2019_2020_specific_primary.csv + + generate_dataset_children_and_adolescents_s5_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2020_2021_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2020_2021.arrow + -- children_and_adolescents season5_start_date season5_end_date specific primary children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2020_2021_specific_primary.arrow + + process_dataset_children_and_adolescents_s5_specific_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season5_start_date + season5_end_date specific primary children_and_adolescents s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - generate_dataset_children_and_adolescents_s5_specific_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2020_2021_specific_primary.arrow + + describe_dataset_children_and_adolescents_s5_specific_primary: + run: r:latest analysis/report.R children_and_adolescents season5_start_date season5_end_date + specific primary children_and_adolescents s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date specific primary + children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season5_start_date season5_end_date specific primary children_and_adolescents + s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2020_2021_specific_primary.csv + + generate_dataset_children_and_adolescents_s6_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2021_2022_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2021_2022.arrow + -- children_and_adolescents season6_start_date season6_end_date specific primary children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2021_2022_specific_primary.arrow + + process_dataset_children_and_adolescents_s6_specific_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season6_start_date + season6_end_date specific primary children_and_adolescents s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - generate_dataset_children_and_adolescents_s6_specific_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2021_2022_specific_primary.arrow + + describe_dataset_children_and_adolescents_s6_specific_primary: + run: r:latest analysis/report.R children_and_adolescents season6_start_date season6_end_date + specific primary children_and_adolescents s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date specific primary + children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season6_start_date season6_end_date specific primary children_and_adolescents + s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2021_2022_specific_primary.csv + + generate_dataset_children_and_adolescents_s7_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2022_2023_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow + -- children_and_adolescents season7_start_date season7_end_date specific primary children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2022_2023_specific_primary.arrow + + process_dataset_children_and_adolescents_s7_specific_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season7_start_date + season7_end_date specific primary children_and_adolescents s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - generate_dataset_children_and_adolescents_s7_specific_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2022_2023_specific_primary.arrow + + describe_dataset_children_and_adolescents_s7_specific_primary: + run: r:latest analysis/report.R children_and_adolescents season7_start_date season7_end_date + specific primary children_and_adolescents s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date specific primary + children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season7_start_date season7_end_date specific primary children_and_adolescents + s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2022_2023_specific_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Infants, Codelist Type: Specific, Investigation Type: Primary + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_infants_s1_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2016_2017_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow + -- infants season1_start_date season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2016_2017_specific_primary.arrow + + process_dataset_infants_s1_specific_primary: + run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date + specific primary infants s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - generate_dataset_infants_s1_specific_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2016_2017_specific_primary.arrow + + describe_dataset_infants_s1_specific_primary: + run: r:latest analysis/report.R infants season1_start_date season1_end_date specific + primary infants s1 2016_2017 specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season1_start_date season1_end_date specific primary infants s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season1_start_date season1_end_date specific primary infants s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season1_start_date season1_end_date specific primary infants s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season1_start_date season1_end_date specific primary infants s1 2016_2017 specific + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s1_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_rsv_full_s1_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_flu_full_s1_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season1_start_date + season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2016_2017_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s1_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season1_start_date season1_end_date specific primary infants s1 2016_2017 + specific primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2016_2017_specific_primary.csv + + generate_dataset_infants_s2_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2017_2018_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow + -- infants season2_start_date season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2017_2018_specific_primary.arrow + + process_dataset_infants_s2_specific_primary: + run: r:latest analysis/data_processing.R infants season2_start_date season2_end_date + specific primary infants s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - generate_dataset_infants_s2_specific_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2017_2018_specific_primary.arrow + + describe_dataset_infants_s2_specific_primary: + run: r:latest analysis/report.R infants season2_start_date season2_end_date specific + primary infants s2 2017_2018 specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season2_start_date season2_end_date specific primary infants s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season2_start_date season2_end_date specific primary infants s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season2_start_date season2_end_date specific primary infants s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season2_start_date season2_end_date specific primary infants s2 2017_2018 specific + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_rsv_full_s2_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_flu_full_s2_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season2_start_date + season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2017_2018_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s2_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date specific primary infants s2 2017_2018 + specific primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_primary.csv + + generate_dataset_infants_s3_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2018_2019_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow + -- infants season3_start_date season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2018_2019_specific_primary.arrow + + process_dataset_infants_s3_specific_primary: + run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date + specific primary infants s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - generate_dataset_infants_s3_specific_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2018_2019_specific_primary.arrow + + describe_dataset_infants_s3_specific_primary: + run: r:latest analysis/report.R infants season3_start_date season3_end_date specific + primary infants s3 2018_2019 specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season3_start_date season3_end_date specific primary infants s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season3_start_date season3_end_date specific primary infants s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season3_start_date season3_end_date specific primary infants s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season3_start_date season3_end_date specific primary infants s3 2018_2019 specific + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_rsv_full_s3_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_flu_full_s3_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s3_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_primary.csv + + generate_dataset_infants_s4_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2019_2020_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow + -- infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2019_2020_specific_primary.arrow + + process_dataset_infants_s4_specific_primary: + run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date + specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - generate_dataset_infants_s4_specific_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2019_2020_specific_primary.arrow + + describe_dataset_infants_s4_specific_primary: + run: r:latest analysis/report.R infants season4_start_date season4_end_date specific + primary infants s4 2019_2020 specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_rsv_full_s4_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_flu_full_s4_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s4_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + + analyse_dataset_infants_further_covid_full_s4_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2019_2020_specific_primary.csv + + generate_dataset_infants_s5_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2020_2021_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow + -- infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2020_2021_specific_primary.arrow + + process_dataset_infants_s5_specific_primary: + run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date + specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - generate_dataset_infants_s5_specific_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2020_2021_specific_primary.arrow + + describe_dataset_infants_s5_specific_primary: + run: r:latest analysis/report.R infants season5_start_date season5_end_date specific + primary infants s5 2020_2021 specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_rsv_full_s5_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_flu_full_s5_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s5_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date specific primary infants s5 2020_2021 + specific primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + + analyse_dataset_infants_further_covid_full_s5_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_specific_primary.csv + + generate_dataset_infants_s6_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2021_2022_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2021_2022.arrow + -- infants season6_start_date season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2021_2022_specific_primary.arrow + + process_dataset_infants_s6_specific_primary: + run: r:latest analysis/data_processing.R infants season6_start_date season6_end_date + specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - generate_dataset_infants_s6_specific_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2021_2022_specific_primary.arrow + + describe_dataset_infants_s6_specific_primary: + run: r:latest analysis/report.R infants season6_start_date season6_end_date specific + primary infants s6 2021_2022 specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_rsv_full_s6_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_flu_full_s6_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s6_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date specific primary infants s6 2021_2022 + specific primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + + analyse_dataset_infants_further_covid_full_s6_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season6_start_date + season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2021_2022_specific_primary.csv + + generate_dataset_infants_s7_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2022_2023_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow + -- infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2022_2023_specific_primary.arrow + + process_dataset_infants_s7_specific_primary: + run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date + specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - generate_dataset_infants_s7_specific_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2022_2023_specific_primary.arrow + + describe_dataset_infants_s7_specific_primary: + run: r:latest analysis/report.R infants season7_start_date season7_end_date specific + primary infants s7 2022_2023 specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_rsv_full_s7_specific_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_flu_full_s7_specific_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s7_specific_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date specific primary infants s7 2022_2023 + specific primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + + analyse_dataset_infants_further_covid_full_s7_specific_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season7_start_date + season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2022_2023_specific_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## SENSITIVITY ANALYSES + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults, Codelist Type: Sensitive, Investigation Type: Primary + + + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_older_adults_s1_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2016_2017_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow + -- older_adults season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2016_2017_sensitive_primary.arrow + + process_dataset_older_adults_s1_sensitive_primary: + run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date + sensitive primary older_adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - generate_dataset_older_adults_s1_sensitive_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2016_2017_sensitive_primary.arrow + + describe_dataset_older_adults_s1_sensitive_primary: + run: r:latest analysis/report.R older_adults season1_start_date season1_end_date + sensitive primary older_adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season1_start_date + season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season1_start_date season1_end_date sensitive primary older_adults + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2016_2017_sensitive_primary.csv + + generate_dataset_older_adults_s2_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2017_2018_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2017_2018.arrow + -- older_adults season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2017_2018_sensitive_primary.arrow + + process_dataset_older_adults_s2_sensitive_primary: + run: r:latest analysis/data_processing.R older_adults season2_start_date season2_end_date + sensitive primary older_adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - generate_dataset_older_adults_s2_sensitive_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2017_2018_sensitive_primary.arrow + + describe_dataset_older_adults_s2_sensitive_primary: + run: r:latest analysis/report.R older_adults season2_start_date season2_end_date + sensitive primary older_adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season2_start_date + season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season2_start_date season2_end_date sensitive primary older_adults + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2017_2018_sensitive_primary.csv + + generate_dataset_older_adults_s3_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2018_2019_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2018_2019.arrow + -- older_adults season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2018_2019_sensitive_primary.arrow + + process_dataset_older_adults_s3_sensitive_primary: + run: r:latest analysis/data_processing.R older_adults season3_start_date season3_end_date + sensitive primary older_adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - generate_dataset_older_adults_s3_sensitive_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2018_2019_sensitive_primary.arrow + + describe_dataset_older_adults_s3_sensitive_primary: + run: r:latest analysis/report.R older_adults season3_start_date season3_end_date + sensitive primary older_adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season3_start_date + season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season3_start_date season3_end_date sensitive primary older_adults + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2018_2019_sensitive_primary.csv + + generate_dataset_older_adults_s4_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2019_2020_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2019_2020.arrow + -- older_adults season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2019_2020_sensitive_primary.arrow + + process_dataset_older_adults_s4_sensitive_primary: + run: r:latest analysis/data_processing.R older_adults season4_start_date season4_end_date + sensitive primary older_adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - generate_dataset_older_adults_s4_sensitive_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2019_2020_sensitive_primary.arrow + + describe_dataset_older_adults_s4_sensitive_primary: + run: r:latest analysis/report.R older_adults season4_start_date season4_end_date + sensitive primary older_adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season4_start_date + season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive primary older_adults + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2019_2020_sensitive_primary.csv + + generate_dataset_older_adults_s5_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2020_2021_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2020_2021.arrow + -- older_adults season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2020_2021_sensitive_primary.arrow + + process_dataset_older_adults_s5_sensitive_primary: + run: r:latest analysis/data_processing.R older_adults season5_start_date season5_end_date + sensitive primary older_adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - generate_dataset_older_adults_s5_sensitive_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2020_2021_sensitive_primary.arrow + + describe_dataset_older_adults_s5_sensitive_primary: + run: r:latest analysis/report.R older_adults season5_start_date season5_end_date + sensitive primary older_adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season5_start_date + season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive primary older_adults + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2020_2021_sensitive_primary.csv + + generate_dataset_older_adults_s6_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2021_2022_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2021_2022.arrow + -- older_adults season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2021_2022_sensitive_primary.arrow + + process_dataset_older_adults_s6_sensitive_primary: + run: r:latest analysis/data_processing.R older_adults season6_start_date season6_end_date + sensitive primary older_adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - generate_dataset_older_adults_s6_sensitive_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2021_2022_sensitive_primary.arrow + + describe_dataset_older_adults_s6_sensitive_primary: + run: r:latest analysis/report.R older_adults season6_start_date season6_end_date + sensitive primary older_adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season6_start_date + season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive primary older_adults + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2021_2022_sensitive_primary.csv + + generate_dataset_older_adults_s7_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2022_2023_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2022_2023.arrow + -- older_adults season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2022_2023_sensitive_primary.arrow + + process_dataset_older_adults_s7_sensitive_primary: + run: r:latest analysis/data_processing.R older_adults season7_start_date season7_end_date + sensitive primary older_adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - generate_dataset_older_adults_s7_sensitive_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2022_2023_sensitive_primary.arrow + + describe_dataset_older_adults_s7_sensitive_primary: + run: r:latest analysis/report.R older_adults season7_start_date season7_end_date + sensitive primary older_adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R older_adults season7_start_date + season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adultsfurther__covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive primary older_adults + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_older_adults_further_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R older_adults + season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_older_adults_2022_2023_sensitive_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Adults, Codelist Type: Sensitive, Investigation Type: Primary + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_adults_s1_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2016_2017_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow + -- adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2016_2017_sensitive_primary.arrow + + process_dataset_adults_s1_sensitive_primary: + run: r:latest analysis/data_processing.R adults season1_start_date season1_end_date + sensitive primary adults s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - generate_dataset_adults_s1_sensitive_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2016_2017_sensitive_primary.arrow + + describe_dataset_adults_s1_sensitive_primary: + run: r:latest analysis/report.R adults season1_start_date season1_end_date sensitive + primary adults s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season1_start_date season1_end_date sensitive primary adults s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season1_start_date season1_end_date sensitive primary adults s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season1_start_date season1_end_date sensitive primary adults s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season1_start_date season1_end_date sensitive primary adults s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season1_start_date + season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2016_2017_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2016_2017_sensitive_primary.csv + + generate_dataset_adults_s2_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2017_2018_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2017_2018.arrow + -- adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2017_2018_sensitive_primary.arrow + + process_dataset_adults_s2_sensitive_primary: + run: r:latest analysis/data_processing.R adults season2_start_date season2_end_date + sensitive primary adults s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - generate_dataset_adults_s2_sensitive_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2017_2018_sensitive_primary.arrow + + describe_dataset_adults_s2_sensitive_primary: + run: r:latest analysis/report.R adults season2_start_date season2_end_date sensitive + primary adults s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season2_start_date season2_end_date sensitive primary adults s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season2_start_date season2_end_date sensitive primary adults s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season2_start_date season2_end_date sensitive primary adults s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season2_start_date season2_end_date sensitive primary adults s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season2_start_date + season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2017_2018_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2017_2018_sensitive_primary.csv + + generate_dataset_adults_s3_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2018_2019_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2018_2019.arrow + -- adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2018_2019_sensitive_primary.arrow + + process_dataset_adults_s3_sensitive_primary: + run: r:latest analysis/data_processing.R adults season3_start_date season3_end_date + sensitive primary adults s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - generate_dataset_adults_s3_sensitive_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2018_2019_sensitive_primary.arrow + + describe_dataset_adults_s3_sensitive_primary: + run: r:latest analysis/report.R adults season3_start_date season3_end_date sensitive + primary adults s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season3_start_date season3_end_date sensitive primary adults s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season3_start_date season3_end_date sensitive primary adults s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season3_start_date season3_end_date sensitive primary adults s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season3_start_date season3_end_date sensitive primary adults s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season3_start_date + season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2018_2019_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2018_2019_sensitive_primary.csv + + generate_dataset_adults_s4_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2019_2020_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2019_2020.arrow + -- adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2019_2020_sensitive_primary.arrow + + process_dataset_adults_s4_sensitive_primary: + run: r:latest analysis/data_processing.R adults season4_start_date season4_end_date + sensitive primary adults s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - generate_dataset_adults_s4_sensitive_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2019_2020_sensitive_primary.arrow + + describe_dataset_adults_s4_sensitive_primary: + run: r:latest analysis/report.R adults season4_start_date season4_end_date sensitive + primary adults s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_primary.csv + + analyse_dataset_adults_further_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season4_start_date + season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2019_2020_sensitive_primary.csv + + generate_dataset_adults_s5_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2020_2021_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2020_2021.arrow + -- adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2020_2021_sensitive_primary.arrow + + process_dataset_adults_s5_sensitive_primary: + run: r:latest analysis/data_processing.R adults season5_start_date season5_end_date + sensitive primary adults s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - generate_dataset_adults_s5_sensitive_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2020_2021_sensitive_primary.arrow + + describe_dataset_adults_s5_sensitive_primary: + run: r:latest analysis/report.R adults season5_start_date season5_end_date sensitive + primary adults s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_primary.csv + + analyse_dataset_adults_further_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season5_start_date + season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2020_2021_sensitive_primary.csv + + generate_dataset_adults_s6_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2021_2022_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2021_2022.arrow + -- adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2021_2022_sensitive_primary.arrow + + process_dataset_adults_s6_sensitive_primary: + run: r:latest analysis/data_processing.R adults season6_start_date season6_end_date + sensitive primary adults s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - generate_dataset_adults_s6_sensitive_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2021_2022_sensitive_primary.arrow + + describe_dataset_adults_s6_sensitive_primary: + run: r:latest analysis/report.R adults season6_start_date season6_end_date sensitive + primary adults s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_primary.csv + + analyse_dataset_adults_further_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season6_start_date + season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2021_2022_sensitive_primary.csv + + generate_dataset_adults_s7_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2022_2023_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow + -- adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2022_2023_sensitive_primary.arrow + + process_dataset_adults_s7_sensitive_primary: + run: r:latest analysis/data_processing.R adults season7_start_date season7_end_date + sensitive primary adults s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - generate_dataset_adults_s7_sensitive_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2022_2023_sensitive_primary.arrow + + describe_dataset_adults_s7_sensitive_primary: + run: r:latest analysis/report.R adults season7_start_date season7_end_date sensitive + primary adults s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adultsfurther__covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R adults + season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_primary.csv + + analyse_dataset_adults_further_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R adults season7_start_date + season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_adults_2022_2023_sensitive_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Children and Adolescents, Codelist Type: Sensitive, Investigation + Type: Primary + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_children_and_adolescents_s1_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2016_2017_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow + -- children_and_adolescents season1_start_date season1_end_date sensitive primary children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2016_2017_sensitive_primary.arrow + + process_dataset_children_and_adolescents_s1_sensitive_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season1_start_date + season1_end_date sensitive primary children_and_adolescents s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - generate_dataset_children_and_adolescents_s1_sensitive_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2016_2017_sensitive_primary.arrow + + describe_dataset_children_and_adolescents_s1_sensitive_primary: + run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date + sensitive primary children_and_adolescents s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive primary children_and_adolescents + s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season1_start_date season1_end_date sensitive primary + children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2016_2017_sensitive_primary.csv + + generate_dataset_children_and_adolescents_s2_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2017_2018_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2017_2018.arrow + -- children_and_adolescents season2_start_date season2_end_date sensitive primary children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2017_2018_sensitive_primary.arrow + + process_dataset_children_and_adolescents_s2_sensitive_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season2_start_date + season2_end_date sensitive primary children_and_adolescents s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - generate_dataset_children_and_adolescents_s2_sensitive_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2017_2018_sensitive_primary.arrow + + describe_dataset_children_and_adolescents_s2_sensitive_primary: + run: r:latest analysis/report.R children_and_adolescents season2_start_date season2_end_date + sensitive primary children_and_adolescents s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive primary children_and_adolescents + s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season2_start_date season2_end_date sensitive primary + children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2017_2018_sensitive_primary.csv + + generate_dataset_children_and_adolescents_s3_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2018_2019_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2018_2019.arrow + -- children_and_adolescents season3_start_date season3_end_date sensitive primary children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2018_2019_sensitive_primary.arrow + + process_dataset_children_and_adolescents_s3_sensitive_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season3_start_date + season3_end_date sensitive primary children_and_adolescents s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - generate_dataset_children_and_adolescents_s3_sensitive_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2018_2019_sensitive_primary.arrow + + describe_dataset_children_and_adolescents_s3_sensitive_primary: + run: r:latest analysis/report.R children_and_adolescents season3_start_date season3_end_date + sensitive primary children_and_adolescents s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive primary children_and_adolescents + s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season3_start_date season3_end_date sensitive primary + children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2018_2019_sensitive_primary.csv + + generate_dataset_children_and_adolescents_s4_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2019_2020_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2019_2020.arrow + -- children_and_adolescents season4_start_date season4_end_date sensitive primary children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2019_2020_sensitive_primary.arrow + + process_dataset_children_and_adolescents_s4_sensitive_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season4_start_date + season4_end_date sensitive primary children_and_adolescents s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - generate_dataset_children_and_adolescents_s4_sensitive_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2019_2020_sensitive_primary.arrow + + describe_dataset_children_and_adolescents_s4_sensitive_primary: + run: r:latest analysis/report.R children_and_adolescents season4_start_date season4_end_date + sensitive primary children_and_adolescents s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive primary + children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive primary children_and_adolescents + s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2019_2020_sensitive_primary.csv + + generate_dataset_children_and_adolescents_s5_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2020_2021_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2020_2021.arrow + -- children_and_adolescents season5_start_date season5_end_date sensitive primary children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2020_2021_sensitive_primary.arrow + + process_dataset_children_and_adolescents_s5_sensitive_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season5_start_date + season5_end_date sensitive primary children_and_adolescents s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - generate_dataset_children_and_adolescents_s5_sensitive_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2020_2021_sensitive_primary.arrow + + describe_dataset_children_and_adolescents_s5_sensitive_primary: + run: r:latest analysis/report.R children_and_adolescents season5_start_date season5_end_date + sensitive primary children_and_adolescents s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive primary + children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive primary children_and_adolescents + s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2020_2021_sensitive_primary.csv + + generate_dataset_children_and_adolescents_s6_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2021_2022_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2021_2022.arrow + -- children_and_adolescents season6_start_date season6_end_date sensitive primary children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2021_2022_sensitive_primary.arrow + + process_dataset_children_and_adolescents_s6_sensitive_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season6_start_date + season6_end_date sensitive primary children_and_adolescents s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - generate_dataset_children_and_adolescents_s6_sensitive_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2021_2022_sensitive_primary.arrow + + describe_dataset_children_and_adolescents_s6_sensitive_primary: + run: r:latest analysis/report.R children_and_adolescents season6_start_date season6_end_date + sensitive primary children_and_adolescents s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive primary + children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive primary children_and_adolescents + s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2021_2022_sensitive_primary.csv + + generate_dataset_children_and_adolescents_s7_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2022_2023_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow + -- children_and_adolescents season7_start_date season7_end_date sensitive primary children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2022_2023_sensitive_primary.arrow + + process_dataset_children_and_adolescents_s7_sensitive_primary: + run: r:latest analysis/data_processing.R children_and_adolescents season7_start_date + season7_end_date sensitive primary children_and_adolescents s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - generate_dataset_children_and_adolescents_s7_sensitive_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2022_2023_sensitive_primary.arrow + + describe_dataset_children_and_adolescents_s7_sensitive_primary: + run: r:latest analysis/report.R children_and_adolescents season7_start_date season7_end_date + sensitive primary children_and_adolescents s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescentsfurther__covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive primary + children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + analyse_dataset_children_and_adolescents_further_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive primary children_and_adolescents + s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_children_and_adolescents_2022_2023_sensitive_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Infants, Codelist Type: Sensitive, Investigation Type: Primary + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_infants_s1_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2016_2017_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow + -- infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2016_2017_sensitive_primary.arrow + + process_dataset_infants_s1_sensitive_primary: + run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date + sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - generate_dataset_infants_s1_sensitive_primary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2016_2017_sensitive_primary.arrow + + describe_dataset_infants_s1_sensitive_primary: + run: r:latest analysis/report.R infants season1_start_date season1_end_date sensitive + primary infants s1 2016_2017 sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive + primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_full_s1_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_flu_full_s1_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season1_start_date + season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2016_2017_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s1_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 + sensitive primary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_primary.csv + + generate_dataset_infants_s2_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2017_2018_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow + -- infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2017_2018_sensitive_primary.arrow + + process_dataset_infants_s2_sensitive_primary: + run: r:latest analysis/data_processing.R infants season2_start_date season2_end_date + sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - generate_dataset_infants_s2_sensitive_primary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2017_2018_sensitive_primary.arrow + + describe_dataset_infants_s2_sensitive_primary: + run: r:latest analysis/report.R infants season2_start_date season2_end_date sensitive + primary infants s2 2017_2018 sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive + primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_full_s2_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_flu_full_s2_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season2_start_date + season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2017_2018_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s2_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 + sensitive primary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_primary.csv + + generate_dataset_infants_s3_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2018_2019_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow + -- infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2018_2019_sensitive_primary.arrow + + process_dataset_infants_s3_sensitive_primary: + run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date + sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - generate_dataset_infants_s3_sensitive_primary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2018_2019_sensitive_primary.arrow + + describe_dataset_infants_s3_sensitive_primary: + run: r:latest analysis/report.R infants season3_start_date season3_end_date sensitive + primary infants s3 2018_2019 sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive + primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_full_s3_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_flu_full_s3_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s3_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_primary.csv + + generate_dataset_infants_s4_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2019_2020_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow + -- infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2019_2020_sensitive_primary.arrow + + process_dataset_infants_s4_sensitive_primary: + run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date + sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - generate_dataset_infants_s4_sensitive_primary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2019_2020_sensitive_primary.arrow + + describe_dataset_infants_s4_sensitive_primary: + run: r:latest analysis/report.R infants season4_start_date season4_end_date sensitive + primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_full_s4_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_flu_full_s4_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s4_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + + analyse_dataset_infants_further_covid_full_s4_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2019_2020_sensitive_primary.csv + + generate_dataset_infants_s5_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2020_2021_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow + -- infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2020_2021_sensitive_primary.arrow + + process_dataset_infants_s5_sensitive_primary: + run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date + sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - generate_dataset_infants_s5_sensitive_primary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2020_2021_sensitive_primary.arrow + + describe_dataset_infants_s5_sensitive_primary: + run: r:latest analysis/report.R infants season5_start_date season5_end_date sensitive + primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_full_s5_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_flu_full_s5_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s5_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 + sensitive primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + + analyse_dataset_infants_further_covid_full_s5_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_sensitive_primary.csv + + generate_dataset_infants_s6_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2021_2022_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2021_2022.arrow + -- infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2021_2022_sensitive_primary.arrow + + process_dataset_infants_s6_sensitive_primary: + run: r:latest analysis/data_processing.R infants season6_start_date season6_end_date + sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - generate_dataset_infants_s6_sensitive_primary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2021_2022_sensitive_primary.arrow + + describe_dataset_infants_s6_sensitive_primary: + run: r:latest analysis/report.R infants season6_start_date season6_end_date sensitive + primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_full_s6_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_flu_full_s6_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s6_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 + sensitive primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + + analyse_dataset_infants_further_covid_full_s6_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season6_start_date + season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2021_2022_sensitive_primary.csv + + generate_dataset_infants_s7_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2022_2023_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow + -- infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2022_2023_sensitive_primary.arrow + + process_dataset_infants_s7_sensitive_primary: + run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date + sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - generate_dataset_infants_s7_sensitive_primary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2022_2023_sensitive_primary.arrow + + describe_dataset_infants_s7_sensitive_primary: + run: r:latest analysis/report.R infants season7_start_date season7_end_date sensitive + primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_flu_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_rsv_full_s7_sensitive_primary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_flu_full_s7_sensitive_primary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s7_sensitive_primary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/covid_full_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/covid_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infantsfurther__covid_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_hh_comp_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_ses_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 + sensitive primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_ses_hh_comp_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + + analyse_dataset_infants_further_covid_full_s7_sensitive_primary: + run: r:latest analysis/covid_specific/further_covid_full_models.R infants season7_start_date + season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/models/further_covid_full_model_outputs_infants_2022_2023_sensitive_primary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## SECONDARY ANALYSES + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults, Codelist Type: Sensitive, Investigation Type: Secondary + + + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_older_adults_s1_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2016_2017_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow + -- older_adults season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2016_2017_sensitive_secondary.arrow + + process_dataset_older_adults_s1_sensitive_secondary: + run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date + sensitive secondary older_adults s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - generate_dataset_older_adults_s1_sensitive_secondary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2016_2017_sensitive_secondary.arrow + + describe_dataset_older_adults_s1_sensitive_secondary: + run: r:latest analysis/report.R older_adults season1_start_date season1_end_date + sensitive secondary older_adults s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season1_start_date season1_end_date sensitive secondary older_adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season1_start_date + season1_end_date sensitive secondary older_adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season1_start_date season1_end_date sensitive secondary older_adults + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2016_2017_sensitive_secondary.csv + + generate_dataset_older_adults_s2_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2017_2018_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2017_2018.arrow + -- older_adults season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2017_2018_sensitive_secondary.arrow + + process_dataset_older_adults_s2_sensitive_secondary: + run: r:latest analysis/data_processing.R older_adults season2_start_date season2_end_date + sensitive secondary older_adults s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - generate_dataset_older_adults_s2_sensitive_secondary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2017_2018_sensitive_secondary.arrow + + describe_dataset_older_adults_s2_sensitive_secondary: + run: r:latest analysis/report.R older_adults season2_start_date season2_end_date + sensitive secondary older_adults s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season2_start_date season2_end_date sensitive secondary older_adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season2_start_date + season2_end_date sensitive secondary older_adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season2_start_date season2_end_date sensitive secondary older_adults + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2017_2018_sensitive_secondary.csv + + generate_dataset_older_adults_s3_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2018_2019_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2018_2019.arrow + -- older_adults season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2018_2019_sensitive_secondary.arrow + + process_dataset_older_adults_s3_sensitive_secondary: + run: r:latest analysis/data_processing.R older_adults season3_start_date season3_end_date + sensitive secondary older_adults s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - generate_dataset_older_adults_s3_sensitive_secondary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2018_2019_sensitive_secondary.arrow + + describe_dataset_older_adults_s3_sensitive_secondary: + run: r:latest analysis/report.R older_adults season3_start_date season3_end_date + sensitive secondary older_adults s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season3_start_date season3_end_date sensitive secondary older_adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season3_start_date + season3_end_date sensitive secondary older_adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season3_start_date season3_end_date sensitive secondary older_adults + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2018_2019_sensitive_secondary.csv + + generate_dataset_older_adults_s4_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2019_2020_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2019_2020.arrow + -- older_adults season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2019_2020_sensitive_secondary.arrow + + process_dataset_older_adults_s4_sensitive_secondary: + run: r:latest analysis/data_processing.R older_adults season4_start_date season4_end_date + sensitive secondary older_adults s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - generate_dataset_older_adults_s4_sensitive_secondary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2019_2020_sensitive_secondary.arrow + + describe_dataset_older_adults_s4_sensitive_secondary: + run: r:latest analysis/report.R older_adults season4_start_date season4_end_date + sensitive secondary older_adults s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season4_start_date season4_end_date sensitive secondary older_adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season4_start_date + season4_end_date sensitive secondary older_adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season4_start_date season4_end_date sensitive secondary older_adults + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2019_2020_sensitive_secondary.csv + + generate_dataset_older_adults_s5_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2020_2021_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2020_2021.arrow + -- older_adults season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2020_2021_sensitive_secondary.arrow + + process_dataset_older_adults_s5_sensitive_secondary: + run: r:latest analysis/data_processing.R older_adults season5_start_date season5_end_date + sensitive secondary older_adults s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - generate_dataset_older_adults_s5_sensitive_secondary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2020_2021_sensitive_secondary.arrow + + describe_dataset_older_adults_s5_sensitive_secondary: + run: r:latest analysis/report.R older_adults season5_start_date season5_end_date + sensitive secondary older_adults s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season5_start_date season5_end_date sensitive secondary older_adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season5_start_date + season5_end_date sensitive secondary older_adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season5_start_date season5_end_date sensitive secondary older_adults + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2020_2021_sensitive_secondary.csv + + generate_dataset_older_adults_s6_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2021_2022_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2021_2022.arrow + -- older_adults season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2021_2022_sensitive_secondary.arrow + + process_dataset_older_adults_s6_sensitive_secondary: + run: r:latest analysis/data_processing.R older_adults season6_start_date season6_end_date + sensitive secondary older_adults s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - generate_dataset_older_adults_s6_sensitive_secondary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2021_2022_sensitive_secondary.arrow + + describe_dataset_older_adults_s6_sensitive_secondary: + run: r:latest analysis/report.R older_adults season6_start_date season6_end_date + sensitive secondary older_adults s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season6_start_date season6_end_date sensitive secondary older_adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season6_start_date + season6_end_date sensitive secondary older_adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season6_start_date season6_end_date sensitive secondary older_adults + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2021_2022_sensitive_secondary.csv + + generate_dataset_older_adults_s7_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2022_2023_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2022_2023.arrow + -- older_adults season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_older_adults_2022_2023_sensitive_secondary.arrow + + process_dataset_older_adults_s7_sensitive_secondary: + run: r:latest analysis/data_processing.R older_adults season7_start_date season7_end_date + sensitive secondary older_adults s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - generate_dataset_older_adults_s7_sensitive_secondary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_2022_2023_sensitive_secondary.arrow + + describe_dataset_older_adults_s7_sensitive_secondary: + run: r:latest analysis/report.R older_adults season7_start_date season7_end_date + sensitive secondary older_adults s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R older_adults + season7_start_date season7_end_date sensitive secondary older_adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R older_adults season7_start_date + season7_end_date sensitive secondary older_adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_older_adults_further_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + older_adults season7_start_date season7_end_date sensitive secondary older_adults + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_older_adults_2022_2023_sensitive_secondary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Adults, Codelist Type: Sensitive, Investigation Type: Secondary + + + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_adults_s1_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2016_2017_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow + -- adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2016_2017_sensitive_secondary.arrow + + process_dataset_adults_s1_sensitive_secondary: + run: r:latest analysis/data_processing.R adults season1_start_date season1_end_date + sensitive secondary adults s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - generate_dataset_adults_s1_sensitive_secondary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2016_2017_sensitive_secondary.arrow + + describe_dataset_adults_s1_sensitive_secondary: + run: r:latest analysis/report.R adults season1_start_date season1_end_date sensitive + secondary adults s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season1_start_date + season1_end_date sensitive secondary adults s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2016_2017_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season1_start_date season1_end_date sensitive secondary adults s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2016_2017_sensitive_secondary.csv + + generate_dataset_adults_s2_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2017_2018_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2017_2018.arrow + -- adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2017_2018_sensitive_secondary.arrow + + process_dataset_adults_s2_sensitive_secondary: + run: r:latest analysis/data_processing.R adults season2_start_date season2_end_date + sensitive secondary adults s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - generate_dataset_adults_s2_sensitive_secondary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2017_2018_sensitive_secondary.arrow + + describe_dataset_adults_s2_sensitive_secondary: + run: r:latest analysis/report.R adults season2_start_date season2_end_date sensitive + secondary adults s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season2_start_date + season2_end_date sensitive secondary adults s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2017_2018_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season2_start_date season2_end_date sensitive secondary adults s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2017_2018_sensitive_secondary.csv + + generate_dataset_adults_s3_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2018_2019_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2018_2019.arrow + -- adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2018_2019_sensitive_secondary.arrow + + process_dataset_adults_s3_sensitive_secondary: + run: r:latest analysis/data_processing.R adults season3_start_date season3_end_date + sensitive secondary adults s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - generate_dataset_adults_s3_sensitive_secondary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2018_2019_sensitive_secondary.arrow + + describe_dataset_adults_s3_sensitive_secondary: + run: r:latest analysis/report.R adults season3_start_date season3_end_date sensitive + secondary adults s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season3_start_date + season3_end_date sensitive secondary adults s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2018_2019_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season3_start_date season3_end_date sensitive secondary adults s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2018_2019_sensitive_secondary.csv + + generate_dataset_adults_s4_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2019_2020_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2019_2020.arrow + -- adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2019_2020_sensitive_secondary.arrow + + process_dataset_adults_s4_sensitive_secondary: + run: r:latest analysis/data_processing.R adults season4_start_date season4_end_date + sensitive secondary adults s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - generate_dataset_adults_s4_sensitive_secondary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2019_2020_sensitive_secondary.arrow + + describe_dataset_adults_s4_sensitive_secondary: + run: r:latest analysis/report.R adults season4_start_date season4_end_date sensitive + secondary adults s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season4_start_date + season4_end_date sensitive secondary adults s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2019_2020_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season4_start_date season4_end_date sensitive secondary adults s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2019_2020_sensitive_secondary.csv + + generate_dataset_adults_s5_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2020_2021_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2020_2021.arrow + -- adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2020_2021_sensitive_secondary.arrow + + process_dataset_adults_s5_sensitive_secondary: + run: r:latest analysis/data_processing.R adults season5_start_date season5_end_date + sensitive secondary adults s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - generate_dataset_adults_s5_sensitive_secondary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2020_2021_sensitive_secondary.arrow + + describe_dataset_adults_s5_sensitive_secondary: + run: r:latest analysis/report.R adults season5_start_date season5_end_date sensitive + secondary adults s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season5_start_date + season5_end_date sensitive secondary adults s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2020_2021_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season5_start_date season5_end_date sensitive secondary adults s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2020_2021_sensitive_secondary.csv + + generate_dataset_adults_s6_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2021_2022_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2021_2022.arrow + -- adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2021_2022_sensitive_secondary.arrow + + process_dataset_adults_s6_sensitive_secondary: + run: r:latest analysis/data_processing.R adults season6_start_date season6_end_date + sensitive secondary adults s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - generate_dataset_adults_s6_sensitive_secondary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2021_2022_sensitive_secondary.arrow + + describe_dataset_adults_s6_sensitive_secondary: + run: r:latest analysis/report.R adults season6_start_date season6_end_date sensitive + secondary adults s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season6_start_date + season6_end_date sensitive secondary adults s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2021_2022_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season6_start_date season6_end_date sensitive secondary adults s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2021_2022_sensitive_secondary.csv + + generate_dataset_adults_s7_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2022_2023_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow + -- adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_adults_2022_2023_sensitive_secondary.arrow + + process_dataset_adults_s7_sensitive_secondary: + run: r:latest analysis/data_processing.R adults season7_start_date season7_end_date + sensitive secondary adults s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - generate_dataset_adults_s7_sensitive_secondary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_adults_2022_2023_sensitive_secondary.arrow + + describe_dataset_adults_s7_sensitive_secondary: + run: r:latest analysis/report.R adults season7_start_date season7_end_date sensitive + secondary adults s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R adults + season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R adults + season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R adults + season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R adults season7_start_date + season7_end_date sensitive secondary adults s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_adults_2022_2023_sensitive_secondary.csv + + analyse_dataset_adults_further_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + adults season7_start_date season7_end_date sensitive secondary adults s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_adults_2022_2023_sensitive_secondary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Children and Adolescents, Codelist Type: Sensitive, Investigation + Type: Secondary + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_children_and_adolescents_s1_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2016_2017_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow + -- children_and_adolescents season1_start_date season1_end_date sensitive secondary children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2016_2017_sensitive_secondary.arrow + + process_dataset_children_and_adolescents_s1_sensitive_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season1_start_date + season1_end_date sensitive secondary children_and_adolescents s1 2016_2017 sensitive + secondary season1_start_date season1_end_date + needs: + - generate_dataset_children_and_adolescents_s1_sensitive_secondary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2016_2017_sensitive_secondary.arrow + + describe_dataset_children_and_adolescents_s1_sensitive_secondary: + run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date + sensitive secondary children_and_adolescents s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season1_start_date season1_end_date sensitive secondary children_and_adolescents + s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season1_start_date season1_end_date sensitive secondary + children_and_adolescents s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2016_2017_sensitive_secondary.csv + + generate_dataset_children_and_adolescents_s2_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2017_2018_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2017_2018.arrow + -- children_and_adolescents season2_start_date season2_end_date sensitive secondary children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2017_2018_sensitive_secondary.arrow + + process_dataset_children_and_adolescents_s2_sensitive_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season2_start_date + season2_end_date sensitive secondary children_and_adolescents s2 2017_2018 sensitive + secondary season2_start_date season2_end_date + needs: + - generate_dataset_children_and_adolescents_s2_sensitive_secondary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2017_2018_sensitive_secondary.arrow + + describe_dataset_children_and_adolescents_s2_sensitive_secondary: + run: r:latest analysis/report.R children_and_adolescents season2_start_date season2_end_date + sensitive secondary children_and_adolescents s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season2_start_date season2_end_date sensitive secondary children_and_adolescents + s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season2_start_date season2_end_date sensitive secondary + children_and_adolescents s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2017_2018_sensitive_secondary.csv + + generate_dataset_children_and_adolescents_s3_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2018_2019_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2018_2019.arrow + -- children_and_adolescents season3_start_date season3_end_date sensitive secondary children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2018_2019_sensitive_secondary.arrow + + process_dataset_children_and_adolescents_s3_sensitive_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season3_start_date + season3_end_date sensitive secondary children_and_adolescents s3 2018_2019 sensitive + secondary season3_start_date season3_end_date + needs: + - generate_dataset_children_and_adolescents_s3_sensitive_secondary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2018_2019_sensitive_secondary.arrow + + describe_dataset_children_and_adolescents_s3_sensitive_secondary: + run: r:latest analysis/report.R children_and_adolescents season3_start_date season3_end_date + sensitive secondary children_and_adolescents s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season3_start_date season3_end_date sensitive secondary children_and_adolescents + s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season3_start_date season3_end_date sensitive secondary + children_and_adolescents s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2018_2019_sensitive_secondary.csv + + generate_dataset_children_and_adolescents_s4_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2019_2020_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2019_2020.arrow + -- children_and_adolescents season4_start_date season4_end_date sensitive secondary children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2019_2020_sensitive_secondary.arrow + + process_dataset_children_and_adolescents_s4_sensitive_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season4_start_date + season4_end_date sensitive secondary children_and_adolescents s4 2019_2020 sensitive + secondary season4_start_date season4_end_date + needs: + - generate_dataset_children_and_adolescents_s4_sensitive_secondary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2019_2020_sensitive_secondary.arrow + + describe_dataset_children_and_adolescents_s4_sensitive_secondary: + run: r:latest analysis/report.R children_and_adolescents season4_start_date season4_end_date + sensitive secondary children_and_adolescents s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season4_start_date season4_end_date sensitive secondary children_and_adolescents + s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season4_start_date season4_end_date sensitive secondary + children_and_adolescents s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2019_2020_sensitive_secondary.csv + + generate_dataset_children_and_adolescents_s5_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2020_2021_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2020_2021.arrow + -- children_and_adolescents season5_start_date season5_end_date sensitive secondary children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2020_2021_sensitive_secondary.arrow + + process_dataset_children_and_adolescents_s5_sensitive_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season5_start_date + season5_end_date sensitive secondary children_and_adolescents s5 2020_2021 sensitive + secondary season5_start_date season5_end_date + needs: + - generate_dataset_children_and_adolescents_s5_sensitive_secondary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2020_2021_sensitive_secondary.arrow + + describe_dataset_children_and_adolescents_s5_sensitive_secondary: + run: r:latest analysis/report.R children_and_adolescents season5_start_date season5_end_date + sensitive secondary children_and_adolescents s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season5_start_date season5_end_date sensitive secondary children_and_adolescents + s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season5_start_date season5_end_date sensitive secondary + children_and_adolescents s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2020_2021_sensitive_secondary.csv + + generate_dataset_children_and_adolescents_s6_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2021_2022_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2021_2022.arrow + -- children_and_adolescents season6_start_date season6_end_date sensitive secondary children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2021_2022_sensitive_secondary.arrow + + process_dataset_children_and_adolescents_s6_sensitive_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season6_start_date + season6_end_date sensitive secondary children_and_adolescents s6 2021_2022 sensitive + secondary season6_start_date season6_end_date + needs: + - generate_dataset_children_and_adolescents_s6_sensitive_secondary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2021_2022_sensitive_secondary.arrow + + describe_dataset_children_and_adolescents_s6_sensitive_secondary: + run: r:latest analysis/report.R children_and_adolescents season6_start_date season6_end_date + sensitive secondary children_and_adolescents s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season6_start_date season6_end_date sensitive secondary children_and_adolescents + s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season6_start_date season6_end_date sensitive secondary + children_and_adolescents s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2021_2022_sensitive_secondary.csv + + generate_dataset_children_and_adolescents_s7_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2022_2023_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow + -- children_and_adolescents season7_start_date season7_end_date sensitive secondary children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2022_2023_sensitive_secondary.arrow + + process_dataset_children_and_adolescents_s7_sensitive_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season7_start_date + season7_end_date sensitive secondary children_and_adolescents s7 2022_2023 sensitive + secondary season7_start_date season7_end_date + needs: + - generate_dataset_children_and_adolescents_s7_sensitive_secondary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2022_2023_sensitive_secondary.arrow + + describe_dataset_children_and_adolescents_s7_sensitive_secondary: + run: r:latest analysis/report.R children_and_adolescents season7_start_date season7_end_date + sensitive secondary children_and_adolescents s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R children_and_adolescents + season7_start_date season7_end_date sensitive secondary children_and_adolescents + s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + analyse_dataset_children_and_adolescents_further_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + children_and_adolescents season7_start_date season7_end_date sensitive secondary + children_and_adolescents s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_children_and_adolescents_2022_2023_sensitive_secondary.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Infants, Codelist Type: Sensitive, Investigation Type: Secondary + + + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_infants_s1_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2016_2017_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow + -- infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2016_2017_sensitive_secondary.arrow + + process_dataset_infants_s1_sensitive_secondary: + run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date + sensitive secondary infants s1 2016_2017 sensitive secondary season1_start_date + season1_end_date + needs: + - generate_dataset_infants_s1_sensitive_secondary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2016_2017_sensitive_secondary.arrow + + describe_dataset_infants_s1_sensitive_secondary: + run: r:latest analysis/report.R infants season1_start_date season1_end_date sensitive + secondary infants s1 2016_2017 sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_full_s1_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_full_s1_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season1_start_date + season1_end_date sensitive secondary infants s1 2016_2017 sensitive secondary + season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2016_2017_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s1_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season1_start_date season1_end_date sensitive secondary infants s1 2016_2017 + sensitive secondary season1_start_date season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_secondary.csv + + generate_dataset_infants_s2_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2017_2018_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow + -- infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2017_2018_sensitive_secondary.arrow + + process_dataset_infants_s2_sensitive_secondary: + run: r:latest analysis/data_processing.R infants season2_start_date season2_end_date + sensitive secondary infants s2 2017_2018 sensitive secondary season2_start_date + season2_end_date + needs: + - generate_dataset_infants_s2_sensitive_secondary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2017_2018_sensitive_secondary.arrow + + describe_dataset_infants_s2_sensitive_secondary: + run: r:latest analysis/report.R infants season2_start_date season2_end_date sensitive + secondary infants s2 2017_2018 sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_full_s2_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_full_s2_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season2_start_date + season2_end_date sensitive secondary infants s2 2017_2018 sensitive secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2017_2018_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s2_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date sensitive secondary infants s2 2017_2018 + sensitive secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_secondary.csv + + generate_dataset_infants_s3_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2018_2019_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow + -- infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2018_2019_sensitive_secondary.arrow + + process_dataset_infants_s3_sensitive_secondary: + run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date + sensitive secondary infants s3 2018_2019 sensitive secondary season3_start_date + season3_end_date + needs: + - generate_dataset_infants_s3_sensitive_secondary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2018_2019_sensitive_secondary.arrow + + describe_dataset_infants_s3_sensitive_secondary: + run: r:latest analysis/report.R infants season3_start_date season3_end_date sensitive + secondary infants s3 2018_2019 sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_full_s3_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_full_s3_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season3_start_date + season3_end_date sensitive secondary infants s3 2018_2019 sensitive secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s3_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date sensitive secondary infants s3 2018_2019 + sensitive secondary season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_secondary.csv + + generate_dataset_infants_s4_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2019_2020_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow + -- infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2019_2020_sensitive_secondary.arrow + + process_dataset_infants_s4_sensitive_secondary: + run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date + sensitive secondary infants s4 2019_2020 sensitive secondary season4_start_date + season4_end_date + needs: + - generate_dataset_infants_s4_sensitive_secondary + - process_household_information_s4 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2019_2020_sensitive_secondary.arrow + + describe_dataset_infants_s4_sensitive_secondary: + run: r:latest analysis/report.R infants season4_start_date season4_end_date sensitive + secondary infants s4 2019_2020 sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_full_s4_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_full_s4_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season4_start_date + season4_end_date sensitive secondary infants s4 2019_2020 sensitive secondary + season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2019_2020_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s4_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season4_start_date season4_end_date sensitive secondary infants s4 2019_2020 + sensitive secondary season4_start_date season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_secondary.csv + + generate_dataset_infants_s5_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2020_2021_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow + -- infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2020_2021_sensitive_secondary.arrow + + process_dataset_infants_s5_sensitive_secondary: + run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date + sensitive secondary infants s5 2020_2021 sensitive secondary season5_start_date + season5_end_date + needs: + - generate_dataset_infants_s5_sensitive_secondary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2020_2021_sensitive_secondary.arrow + + describe_dataset_infants_s5_sensitive_secondary: + run: r:latest analysis/report.R infants season5_start_date season5_end_date sensitive + secondary infants s5 2020_2021 sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_full_s5_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_full_s5_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season5_start_date + season5_end_date sensitive secondary infants s5 2020_2021 sensitive secondary + season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2020_2021_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s5_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date sensitive secondary infants s5 2020_2021 + sensitive secondary season5_start_date season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_secondary.csv + + generate_dataset_infants_s6_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2021_2022_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2021_2022.arrow + -- infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2021_2022_sensitive_secondary.arrow + + process_dataset_infants_s6_sensitive_secondary: + run: r:latest analysis/data_processing.R infants season6_start_date season6_end_date + sensitive secondary infants s6 2021_2022 sensitive secondary season6_start_date + season6_end_date + needs: + - generate_dataset_infants_s6_sensitive_secondary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2021_2022_sensitive_secondary.arrow + + describe_dataset_infants_s6_sensitive_secondary: + run: r:latest analysis/report.R infants season6_start_date season6_end_date sensitive + secondary infants s6 2021_2022 sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_full_s6_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_flu_full_s6_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season6_start_date + season6_end_date sensitive secondary infants s6 2021_2022 sensitive secondary + season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2021_2022_sensitive_secondary.csv + + analyse_dataset_infants_further_overall_and_all_cause_full_s6_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season6_start_date season6_end_date sensitive secondary infants s6 2021_2022 + sensitive secondary season6_start_date season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_secondary.csv + + generate_dataset_infants_s7_sensitive_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2022_2023_sensitive_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow + -- infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2022_2023_sensitive_secondary.arrow + + process_dataset_infants_s7_sensitive_secondary: + run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date + sensitive secondary infants s7 2022_2023 sensitive secondary season7_start_date + season7_end_date + needs: + - generate_dataset_infants_s7_sensitive_secondary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2022_2023_sensitive_secondary.arrow + + describe_dataset_infants_s7_sensitive_secondary: + run: r:latest analysis/report.R infants season7_start_date season7_end_date sensitive + secondary infants s7 2022_2023 sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_hh_comp_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_ses_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_ses_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_ses_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ethnicity_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ethnicity_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - dataset: output/flow_chart/children_and_adolescents_2016_2017_flow_chart.csv + moderately_sensitive: + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - process_flow_chart_children_and_adolescents_s1: - run: r:latest analysis/cohort_criteria.R children_and_adolescents season1_start_date season1_end_date - needs: [generate_flow_chart_data_children_and_adolescents_s1] + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - cohort: output/flow_chart/flow_chart_processed_children_and_adolescents_2016_2017.csv + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - generate_flow_chart_data_infants_s1: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition_flow_chart.py - --output output/flow_chart/infants_2016_2017_flow_chart.csv - --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow - -- infants season1_start_date season1_end_date + analyse_dataset_infants_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - dataset: output/flow_chart/infants_2016_2017_flow_chart.csv + moderately_sensitive: + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - process_flow_chart_infants_s1: - run: r:latest analysis/cohort_criteria.R infants season1_start_date season1_end_date - needs: [generate_flow_chart_data_infants_s1] + analyse_dataset_infants_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - cohort: output/flow_chart/flow_chart_processed_infants_2016_2017.csv + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv -### household information extraction + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_ses_hh_comp_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv -## season 1 (2016/17) + analyse_dataset_infants_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/rsv_full_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_full_model_outputs_infants_2022_2023_sensitive_secondary.csv - extract_household_information_s1: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition_household.py - --output output/data/input_household_2016_2017.arrow - --dummy-data-file analysis/dummydata/dummyextract_household_2016_2017.arrow - -- season1_start_date season1_end_date + analyse_dataset_infants_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/flu_full_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_household_2016_2017.arrow + moderately_sensitive: + csv: output/results/models/flu_full_model_outputs_infants_2022_2023_sensitive_secondary.csv - process_household_information_s1: - run: r:latest analysis/data_processing_household.R season1_start_date season1_end_date - needs: [extract_household_information_s1] + analyse_dataset_infants_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - arrow: output/data/input_household_processed_2016_2017.arrow + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_secondary.csv -## season 7 (2022/23) + analyse_dataset_infants_further_rsv_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2022_2023_sensitive_secondary.csv -## season 1 (2016/17) + analyse_dataset_infants_further_flu_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2022_2023_sensitive_secondary.csv - extract_household_information_s7: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition_household.py - --output output/data/input_household_2022_2023.arrow - --dummy-data-file analysis/dummydata/dummyextract_household_2022_2023.arrow - -- season7_start_date season7_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_household_2022_2023.arrow + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_sensitive_secondary.csv - process_household_information_s7: - run: r:latest analysis/data_processing_household.R season7_start_date season7_end_date - needs: [extract_household_information_s7] + analyse_dataset_infants_further_rsv_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - arrow: output/data/input_household_processed_2022_2023.arrow + moderately_sensitive: + csv: output/results/models/further_rsv_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv -### primary analysis + analyse_dataset_infants_further_flu_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_flu_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv -## season 1 (2016/17) + analyse_dataset_infants_further_overall_and_all_cause_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv - generate_dataset_older_adults_s1_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_older_adults_2016_2017_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow - -- older_adults season1_start_date season1_end_date specific primary + analyse_dataset_infants_further_rsv_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_older_adults_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - process_dataset_older_adults_s1_spec: - run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date specific primary - needs: [generate_dataset_older_adults_s1_spec, process_household_information_s1] + analyse_dataset_infants_further_flu_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_older_adults_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - describe_dataset_older_adults_s1_spec: - run: r:latest analysis/report.R older_adults season1_start_date season1_end_date specific primary - needs: [process_dataset_older_adults_s1_spec] + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_hh_comp_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_older_adults_2016_2017_specific.csv - - analyse_dataset_older_adults_ethnicity_s1_spec: - run: r:latest analysis/ethnicity_models.R older_adults season1_start_date season1_end_date specific primary - needs: [process_dataset_older_adults_s1_spec] + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv + + analyse_dataset_infants_further_rsv_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_ses_models.R infants + season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_older_adults_2016_2017_specific.csv + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv - analyse_dataset_older_adults_ses_s1_spec: - run: r:latest analysis/ses_models.R older_adults season1_start_date season1_end_date specific primary - needs: [process_dataset_older_adults_s1_spec] + analyse_dataset_infants_further_flu_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_ses_models.R infants + season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_older_adults_2016_2017_specific.csv + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv - analyse_dataset_older_adults_hh_comp_s1_spec: - run: r:latest analysis/hh_comp_models.R older_adults season1_start_date season1_end_date specific primary - needs: [process_dataset_older_adults_s1_spec] + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_ses_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_older_adults_2016_2017_specific.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_secondary.csv - generate_dataset_adults_s1_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_adults_2016_2017_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow - -- adults season1_start_date season1_end_date specific primary + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_adults_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - process_dataset_adults_s1_spec: - run: r:latest analysis/data_processing.R adults season1_start_date season1_end_date specific primary - needs: [generate_dataset_adults_s1_spec, process_household_information_s1] + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_adults_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - describe_dataset_adults_s1_spec: - run: r:latest analysis/report.R adults season1_start_date season1_end_date specific primary - needs: [process_dataset_adults_s1_spec] + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_adults_2016_2017_specific.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - analyse_dataset_adults_ethnicity_s1_spec: - run: r:latest analysis/ethnicity_models.R adults season1_start_date season1_end_date specific primary - needs: [process_dataset_adults_s1_spec] + analyse_dataset_infants_further_rsv_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_adults_2016_2017_specific.csv + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - analyse_dataset_adults_ses_s1_spec: - run: r:latest analysis/ses_models.R adults season1_start_date season1_end_date specific primary - needs: [process_dataset_adults_s1_spec] + analyse_dataset_infants_further_flu_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_ses_hh_comp_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_adults_2016_2017_specific.csv + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - analyse_dataset_adults_hh_comp_s1_spec: - run: r:latest analysis/hh_comp_models.R adults season1_start_date season1_end_date specific primary - needs: [process_dataset_adults_s1_spec] + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_secondary: + run: r:latest analysis/overall_and_all_cause_specific/further_overall_and_all_cause_ses_hh_comp_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_adults_2016_2017_specific.csv + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_secondary.csv - generate_dataset_children_and_adolescents_s1_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2016_2017_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow - -- children_and_adolescents season1_start_date season1_end_date specific primary + analyse_dataset_infants_further_rsv_full_s7_sensitive_secondary: + run: r:latest analysis/rsv_specific/further_rsv_full_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_children_and_adolescents_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/results/models/further_rsv_full_model_outputs_infants_2022_2023_sensitive_secondary.csv - process_dataset_children_and_adolescents_s1_spec: - run: r:latest analysis/data_processing.R children_and_adolescents season1_start_date season1_end_date specific primary - needs: [generate_dataset_children_and_adolescents_s1_spec, process_household_information_s1] + analyse_dataset_infants_further_flu_full_s7_sensitive_secondary: + run: r:latest analysis/flu_specific/further_flu_full_models.R infants season7_start_date + season7_end_date sensitive secondary infants s7 2022_2023 sensitive secondary + season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/results/models/further_flu_full_model_outputs_infants_2022_2023_sensitive_secondary.csv - describe_dataset_children_and_adolescents_s1_spec: - run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date specific primary - needs: [process_dataset_children_and_adolescents_s1_spec] + analyse_dataset_infants_further_overall_and_all_cause_full_s7_sensitive_secondary: + run: r:latest analysis/further_overall_and_all_cause_specific/overall_and_all_cause_full_models.R + infants season7_start_date season7_end_date sensitive secondary infants s7 2022_2023 + sensitive secondary season7_start_date season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2016_2017_specific.csv + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_secondary.csv - analyse_dataset_children_and_adolescents_ethnicity_s1_spec: - run: r:latest analysis/ethnicity_models.R children_and_adolescents season1_start_date season1_end_date specific primary - needs: [process_dataset_children_and_adolescents_s1_spec] + ## # # # # # # # # # # # # # # # # # # # + ## DESCRIPTIVE ANALYSES + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults + ## # # # # # # # # # # # # # # # # # # # + + describe_cohort_older_adults_s1: + run: r:latest analysis/cohort_description.R older_adults season1_start_date season1_end_date + sensitive secondary older_adults s1 2016_2017 specific secondary season1_start_date + season1_end_date + needs: + - process_dataset_older_adults_s1_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_children_and_adolescents_2016_2017_specific.csv + csv: output/table1/table1_older_adults_2016_2017.csv - analyse_dataset_children_and_adolescents_ses_s1_spec: - run: r:latest analysis/ses_models.R children_and_adolescents season1_start_date season1_end_date specific primary - needs: [process_dataset_children_and_adolescents_s1_spec] + describe_cohort_older_adults_s2: + run: r:latest analysis/cohort_description.R older_adults season2_start_date season2_end_date + sensitive secondary older_adults s2 2017_2018 specific secondary season2_start_date + season2_end_date + needs: + - process_dataset_older_adults_s2_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_children_and_adolescents_2016_2017_specific.csv + csv: output/table1/table1_older_adults_2017_2018.csv - analyse_dataset_children_and_adolescents_hh_comp_s1_spec: - run: r:latest analysis/hh_comp_models.R children_and_adolescents season1_start_date season1_end_date specific primary - needs: [process_dataset_children_and_adolescents_s1_spec] + describe_cohort_older_adults_s3: + run: r:latest analysis/cohort_description.R older_adults season3_start_date season3_end_date + sensitive secondary older_adults s3 2018_2019 specific secondary season3_start_date + season3_end_date + needs: + - process_dataset_older_adults_s3_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_children_and_adolescents_2016_2017_specific.csv - - generate_dataset_infants_s1_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2016_2017_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow - -- infants season1_start_date season1_end_date specific primary + csv: output/table1/table1_older_adults_2018_2019.csv + + describe_cohort_older_adults_s4: + run: r:latest analysis/cohort_description.R older_adults season4_start_date season4_end_date + sensitive secondary older_adults s4 2019_2020 specific secondary season4_start_date + season4_end_date + needs: + - process_dataset_older_adults_s4_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_infants_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_older_adults_2019_2020.csv - process_dataset_infants_s1_spec: - run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date specific primary - needs: [generate_dataset_infants_s1_spec, process_household_information_s1] + describe_cohort_older_adults_s5: + run: r:latest analysis/cohort_description.R older_adults season5_start_date season5_end_date + sensitive secondary older_adults s5 2020_2021 specific secondary season5_start_date + season5_end_date + needs: + - process_dataset_older_adults_s5_sensitive_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2016_2017_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_older_adults_2020_2021.csv - describe_dataset_infants_s1_spec: - run: r:latest analysis/report.R infants season1_start_date season1_end_date specific primary - needs: [process_dataset_infants_s1_spec] + describe_cohort_older_adults_s6: + run: r:latest analysis/cohort_description.R older_adults season6_start_date season6_end_date + sensitive secondary older_adults s6 2021_2022 specific secondary season6_start_date + season6_end_date + needs: + - process_dataset_older_adults_s6_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2016_2017_specific.csv - - analyse_dataset_infants_ethnicity_s1_spec: - run: r:latest analysis/ethnicity_models.R infants season1_start_date season1_end_date specific primary - needs: [process_dataset_infants_s1_spec] + csv: output/table1/table1_older_adults_2021_2022.csv + + describe_cohort_older_adults_s7: + run: r:latest analysis/cohort_description.R older_adults season7_start_date season7_end_date + sensitive secondary older_adults s7 2022_2023 specific secondary season7_start_date + season7_end_date + needs: + - process_dataset_older_adults_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_infants_2016_2017_specific.csv + csv: output/table1/table1_older_adults_2022_2023.csv - analyse_dataset_infants_ses_s1_spec: - run: r:latest analysis/ses_models.R infants season1_start_date season1_end_date specific primary - needs: [process_dataset_infants_s1_spec] + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Adults + ## # # # # # # # # # # # # # # # # # # # + + describe_cohort_adults_s1: + run: r:latest analysis/cohort_description.R adults season1_start_date season1_end_date + sensitive secondary adults s1 2016_2017 specific secondary season1_start_date + season1_end_date + needs: + - process_dataset_adults_s1_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_infants_2016_2017_specific.csv + csv: output/table1/table1_adults_2016_2017.csv - analyse_dataset_infants_hh_comp_s1_spec: - run: r:latest analysis/hh_comp_models.R infants season1_start_date season1_end_date specific primary - needs: [process_dataset_infants_s1_spec] + describe_cohort_adults_s2: + run: r:latest analysis/cohort_description.R adults season2_start_date season2_end_date + sensitive secondary adults s2 2017_2018 specific secondary season2_start_date + season2_end_date + needs: + - process_dataset_adults_s2_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_infants_2016_2017_specific.csv + csv: output/table1/table1_adults_2017_2018.csv -# ## season 7 (2022/23) + describe_cohort_adults_s3: + run: r:latest analysis/cohort_description.R adults season3_start_date season3_end_date + sensitive secondary adults s3 2018_2019 specific secondary season3_start_date + season3_end_date + needs: + - process_dataset_adults_s3_sensitive_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_adults_2018_2019.csv - generate_dataset_older_adults_s7_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_older_adults_2022_2023_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_older_adults_2022_2023.arrow - -- older_adults season7_start_date season7_end_date specific primary + describe_cohort_adults_s4: + run: r:latest analysis/cohort_description.R adults season4_start_date season4_end_date + sensitive secondary adults s4 2019_2020 specific secondary season4_start_date + season4_end_date + needs: + - process_dataset_adults_s4_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_older_adults_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_adults_2019_2020.csv - process_dataset_older_adults_s7_spec: - run: r:latest analysis/data_processing.R older_adults season7_start_date season7_end_date specific primary - needs: [generate_dataset_older_adults_s7_spec, process_household_information_s7] + describe_cohort_adults_s5: + run: r:latest analysis/cohort_description.R adults season5_start_date season5_end_date + sensitive secondary adults s5 2020_2021 specific secondary season5_start_date + season5_end_date + needs: + - process_dataset_adults_s5_sensitive_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_older_adults_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_adults_2020_2021.csv - describe_dataset_older_adults_s7_spec: - run: r:latest analysis/report.R older_adults season7_start_date season7_end_date specific primary - needs: [process_dataset_older_adults_s7_spec] + describe_cohort_adults_s6: + run: r:latest analysis/cohort_description.R adults season6_start_date season6_end_date + sensitive secondary adults s6 2021_2022 specific secondary season6_start_date + season6_end_date + needs: + - process_dataset_adults_s6_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_older_adults_2022_2023_specific.csv + csv: output/table1/table1_adults_2021_2022.csv - analyse_dataset_older_adults_ethnicity_s7_spec: - run: r:latest analysis/ethnicity_models.R older_adults season7_start_date season7_end_date specific primary - needs: [process_dataset_older_adults_s7_spec] + describe_cohort_adults_s7: + run: r:latest analysis/cohort_description.R adults season7_start_date season7_end_date + sensitive secondary adults s7 2022_2023 specific secondary season7_start_date + season7_end_date + needs: + - process_dataset_adults_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_older_adults_2022_2023_specific.csv + csv: output/table1/table1_adults_2022_2023.csv - analyse_dataset_older_adults_ses_s7_spec: - run: r:latest analysis/ses_models.R older_adults season7_start_date season7_end_date specific primary - needs: [process_dataset_older_adults_s7_spec] + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Children and Adolescents + ## # # # # # # # # # # # # # # # # # # # + + describe_cohort_children_and_adolescents_s1: + run: r:latest analysis/cohort_description.R children_and_adolescents season1_start_date + season1_end_date sensitive secondary children_and_adolescents s1 2016_2017 specific + secondary season1_start_date season1_end_date + needs: + - process_dataset_children_and_adolescents_s1_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_older_adults_2022_2023_specific.csv + csv: output/table1/table1_children_and_adolescents_2016_2017.csv - analyse_dataset_older_adults_hh_comp_s7_spec: - run: r:latest analysis/hh_comp_models.R older_adults season7_start_date season7_end_date specific primary - needs: [process_dataset_older_adults_s7_spec] + describe_cohort_children_and_adolescents_s2: + run: r:latest analysis/cohort_description.R children_and_adolescents season2_start_date + season2_end_date sensitive secondary children_and_adolescents s2 2017_2018 specific + secondary season2_start_date season2_end_date + needs: + - process_dataset_children_and_adolescents_s2_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_older_adults_2022_2023_specific.csv + csv: output/table1/table1_children_and_adolescents_2017_2018.csv - generate_dataset_adults_s7_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_adults_2022_2023_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow - -- adults season7_start_date season7_end_date specific primary + describe_cohort_children_and_adolescents_s3: + run: r:latest analysis/cohort_description.R children_and_adolescents season3_start_date + season3_end_date sensitive secondary children_and_adolescents s3 2018_2019 specific + secondary season3_start_date season3_end_date + needs: + - process_dataset_children_and_adolescents_s3_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_adults_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_children_and_adolescents_2018_2019.csv - process_dataset_adults_s7_spec: - run: r:latest analysis/data_processing.R adults season7_start_date season7_end_date specific primary - needs: [generate_dataset_adults_s7_spec, process_household_information_s7] + describe_cohort_children_and_adolescents_s4: + run: r:latest analysis/cohort_description.R children_and_adolescents season4_start_date + season4_end_date sensitive secondary children_and_adolescents s4 2019_2020 specific + secondary season4_start_date season4_end_date + needs: + - process_dataset_children_and_adolescents_s4_sensitive_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_adults_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_children_and_adolescents_2019_2020.csv - describe_dataset_adults_s7_spec: - run: r:latest analysis/report.R adults season7_start_date season7_end_date specific primary - needs: [process_dataset_adults_s7_spec] + describe_cohort_children_and_adolescents_s5: + run: r:latest analysis/cohort_description.R children_and_adolescents season5_start_date + season5_end_date sensitive secondary children_and_adolescents s5 2020_2021 specific + secondary season5_start_date season5_end_date + needs: + - process_dataset_children_and_adolescents_s5_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_adults_2022_2023_specific.csv + csv: output/table1/table1_children_and_adolescents_2020_2021.csv - analyse_dataset_adults_ethnicity_s7_spec: - run: r:latest analysis/ethnicity_models.R adults season7_start_date season7_end_date specific primary - needs: [process_dataset_adults_s7_spec] + describe_cohort_children_and_adolescents_s6: + run: r:latest analysis/cohort_description.R children_and_adolescents season6_start_date + season6_end_date sensitive secondary children_and_adolescents s6 2021_2022 specific + secondary season6_start_date season6_end_date + needs: + - process_dataset_children_and_adolescents_s6_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_adults_2022_2023_specific.csv - - analyse_dataset_adults_ses_s7_spec: - run: r:latest analysis/ses_models.R adults season7_start_date season7_end_date specific primary - needs: [process_dataset_adults_s7_spec] + csv: output/table1/table1_children_and_adolescents_2021_2022.csv + + describe_cohort_children_and_adolescents_s7: + run: r:latest analysis/cohort_description.R children_and_adolescents season7_start_date + season7_end_date sensitive secondary children_and_adolescents s7 2022_2023 specific + secondary season7_start_date season7_end_date + needs: + - process_dataset_children_and_adolescents_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_adults_2022_2023_specific.csv + csv: output/table1/table1_children_and_adolescents_2022_2023.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Infants + ## # # # # # # # # # # # # # # # # # # # - analyse_dataset_adults_hh_comp_s7_spec: - run: r:latest analysis/hh_comp_models.R adults season7_start_date season7_end_date specific primary - needs: [process_dataset_adults_s7_spec] + describe_cohort_infants_s1: + run: r:latest analysis/cohort_description.R infants season1_start_date season1_end_date + sensitive secondary infants s1 2016_2017 specific secondary season1_start_date + season1_end_date + needs: + - process_dataset_infants_s1_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_adults_2022_2023_specific.csv + csv: output/table1/table1_infants_2016_2017.csv - generate_dataset_children_and_adolescents_s7_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2022_2023_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow - -- children_and_adolescents season7_start_date season7_end_date specific primary + describe_cohort_infants_s2: + run: r:latest analysis/cohort_description.R infants season2_start_date season2_end_date + sensitive secondary infants s2 2017_2018 specific secondary season2_start_date + season2_end_date + needs: + - process_dataset_infants_s2_sensitive_secondary outputs: - highly_sensitive: - dataset: output/data/input_children_and_adolescents_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_infants_2017_2018.csv - process_dataset_children_and_adolescents_s7_spec: - run: r:latest analysis/data_processing.R children_and_adolescents season7_start_date season7_end_date specific primary - needs: [generate_dataset_children_and_adolescents_s7_spec, process_household_information_s7] + describe_cohort_infants_s3: + run: r:latest analysis/cohort_description.R infants season3_start_date season3_end_date + sensitive secondary infants s3 2018_2019 specific secondary season3_start_date + season3_end_date + needs: + - process_dataset_infants_s3_sensitive_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/table1/table1_infants_2018_2019.csv - describe_dataset_children_and_adolescents_s7_spec: - run: r:latest analysis/report.R children_and_adolescents season7_start_date season7_end_date specific primary - needs: [process_dataset_children_and_adolescents_s7_spec] + describe_cohort_infants_s4: + run: r:latest analysis/cohort_description.R infants season4_start_date season4_end_date + sensitive secondary infants s4 2019_2020 specific secondary season4_start_date + season4_end_date + needs: + - process_dataset_infants_s4_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2022_2023_specific.csv + csv: output/table1/table1_infants_2019_2020.csv - analyse_dataset_children_and_adolescents_ethnicity_s7_spec: - run: r:latest analysis/ethnicity_models.R children_and_adolescents season7_start_date season7_end_date specific primary - needs: [process_dataset_children_and_adolescents_s7_spec] + describe_cohort_infants_s5: + run: r:latest analysis/cohort_description.R infants season5_start_date season5_end_date + sensitive secondary infants s5 2020_2021 specific secondary season5_start_date + season5_end_date + needs: + - process_dataset_infants_s5_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_children_and_adolescents_2022_2023_specific.csv + csv: output/table1/table1_infants_2020_2021.csv - analyse_dataset_children_and_adolescents_ses_s7_spec: - run: r:latest analysis/ses_models.R children_and_adolescents season7_start_date season7_end_date specific primary - needs: [process_dataset_children_and_adolescents_s7_spec] + describe_cohort_infants_s6: + run: r:latest analysis/cohort_description.R infants season6_start_date season6_end_date + sensitive secondary infants s6 2021_2022 specific secondary season6_start_date + season6_end_date + needs: + - process_dataset_infants_s6_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_children_and_adolescents_2022_2023_specific.csv + csv: output/table1/table1_infants_2021_2022.csv - analyse_dataset_children_and_adolescents_hh_comp_s7_spec: - run: r:latest analysis/hh_comp_models.R children_and_adolescents season7_start_date season7_end_date specific primary - needs: [process_dataset_children_and_adolescents_s7_spec] + describe_cohort_infants_s7: + run: r:latest analysis/cohort_description.R infants season7_start_date season7_end_date + sensitive secondary infants s7 2022_2023 specific secondary season7_start_date + season7_end_date + needs: + - process_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_children_and_adolescents_2022_2023_specific.csv + csv: output/table1/table1_infants_2022_2023.csv - generate_dataset_infants_s7_spec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2022_2023_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow - -- infants season7_start_date season7_end_date specific primary + ## # # # # # # # # # # # # # # # # # # # + ## Files for release + ## # # # # # # # # # # # # # # # # # # # + + collate_flow_chart_tables_older_adults: + run: r:latest analysis/flow_chart_table_collation.R older_adults older_adults + needs: + - process_flow_chart_data_older_adults_s1 + - process_flow_chart_data_older_adults_s2 + - process_flow_chart_data_older_adults_s3 + - process_flow_chart_data_older_adults_s4 + - process_flow_chart_data_older_adults_s5 + - process_flow_chart_data_older_adults_s6 + - process_flow_chart_data_older_adults_s7 outputs: - highly_sensitive: - dataset: output/data/input_infants_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/results/collated/older_adults_flow_chart_collated.csv - process_dataset_infants_s7_spec: - run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date specific primary - needs: [generate_dataset_infants_s7_spec, process_household_information_s7] + collate_table1_tables_older_adults: + run: r:latest analysis/table1_table_collation.R older_adults older_adults + needs: + - describe_dataset_older_adults_s1_specific_primary + - describe_dataset_older_adults_s2_specific_primary + - describe_dataset_older_adults_s3_specific_primary + - describe_dataset_older_adults_s4_specific_primary + - describe_dataset_older_adults_s5_specific_primary + - describe_dataset_older_adults_s6_specific_primary + - describe_dataset_older_adults_s7_specific_primary + - describe_dataset_older_adults_s1_sensitive_primary + - describe_dataset_older_adults_s2_sensitive_primary + - describe_dataset_older_adults_s3_sensitive_primary + - describe_dataset_older_adults_s4_sensitive_primary + - describe_dataset_older_adults_s5_sensitive_primary + - describe_dataset_older_adults_s6_sensitive_primary + - describe_dataset_older_adults_s7_sensitive_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2022_2023_specific_primary.arrow + moderately_sensitive: + csv: output/results/collated/older_adults_table1_collated.csv - describe_dataset_infants_s7_spec: - run: r:latest analysis/report.R infants season7_start_date season7_end_date specific primary - needs: [process_dataset_infants_s7_spec] - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2022_2023_specific.csv - - # analyse_dataset_infants_ethnicity_s7_spec: - # run: r:latest analysis/ethnicity_models.R infants season7_start_date season7_end_date specific primary - # needs: [process_dataset_infants_s7_spec] - # outputs: - # moderately_sensitive: - # csv: output/results/models/ethnicity_model_outputs_infants_2022_2023_specific.csv - # - # analyse_dataset_infants_ses_s7_spec: - # run: r:latest analysis/ses_models.R infants season7_start_date season7_end_date specific primary - # needs: [process_dataset_infants_s7_spec] - # outputs: - # moderately_sensitive: - # csv: output/results/models/ses_model_outputs_infants_2022_2023_specific.csv - # - # analyse_dataset_infants_hh_comp_s7_spec: - # run: r:latest analysis/hh_comp_models.R infants season7_start_date season7_end_date specific primary - # needs: [process_dataset_infants_s7_spec] - # outputs: - # moderately_sensitive: - # csv: output/results/models/hh_comp_model_outputs_infants_2022_2023_specific.csv - -### sensitivity analysis - -## season 1 (2016/17) - - generate_dataset_older_adults_s1_sens: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_older_adults_2016_2017_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow - -- older_adults season1_start_date season1_end_date sensitive primary + collate_rates_tables_older_adults: + run: r:latest analysis/rates_table_collation.R older_adults older_adults + needs: + - process_dataset_older_adults_s1_specific_primary + - process_dataset_older_adults_s2_specific_primary + - process_dataset_older_adults_s3_specific_primary + - process_dataset_older_adults_s4_specific_primary + - process_dataset_older_adults_s5_specific_primary + - process_dataset_older_adults_s6_specific_primary + - process_dataset_older_adults_s7_specific_primary + - process_dataset_older_adults_s1_sensitive_primary + - process_dataset_older_adults_s2_sensitive_primary + - process_dataset_older_adults_s3_sensitive_primary + - process_dataset_older_adults_s4_sensitive_primary + - process_dataset_older_adults_s5_sensitive_primary + - process_dataset_older_adults_s6_sensitive_primary + - process_dataset_older_adults_s7_sensitive_primary outputs: - highly_sensitive: - dataset: output/data/input_older_adults_2016_2017_sensitive_primary.arrow + moderately_sensitive: + csv: output/results/collated/older_adults_rates_collated.csv - process_dataset_older_adults_s1_sens: - run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date sensitive primary - needs: [generate_dataset_older_adults_s1_sens, process_household_information_s1] + collate_rsv_model_outputs_tables_older_adults: + run: r:latest analysis/rsv_model_outputs_table_collation.R older_adults older_adults + needs: + - analyse_dataset_older_adults_rsv_ethnicity_s1_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_s2_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_s3_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_s4_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_s5_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_s6_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_s7_specific_primary + - analyse_dataset_older_adults_rsv_ses_s1_specific_primary + - analyse_dataset_older_adults_rsv_ses_s2_specific_primary + - analyse_dataset_older_adults_rsv_ses_s3_specific_primary + - analyse_dataset_older_adults_rsv_ses_s4_specific_primary + - analyse_dataset_older_adults_rsv_ses_s5_specific_primary + - analyse_dataset_older_adults_rsv_ses_s6_specific_primary + - analyse_dataset_older_adults_rsv_ses_s7_specific_primary + - analyse_dataset_older_adults_rsv_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_rsv_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_rsv_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_rsv_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_rsv_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_rsv_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_rsv_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s1_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s2_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s3_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s4_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s5_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s6_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s7_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_rsv_full_s1_specific_primary + - analyse_dataset_older_adults_rsv_full_s2_specific_primary + - analyse_dataset_older_adults_rsv_full_s3_specific_primary + - analyse_dataset_older_adults_rsv_full_s4_specific_primary + - analyse_dataset_older_adults_rsv_full_s5_specific_primary + - analyse_dataset_older_adults_rsv_full_s6_specific_primary + - analyse_dataset_older_adults_rsv_full_s7_specific_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_older_adults_2016_2017_sensitive_primary.arrow + moderately_sensitive: + csv: output/results/collated/older_adults_rsv_model_outputs_collated.csv - describe_dataset_older_adults_s1_sens: - run: r:latest analysis/report.R older_adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_older_adults_s1_sens] + collate_flu_model_outputs_tables_older_adults: + run: r:latest analysis/flu_model_outputs_table_collation.R older_adults older_adults + needs: + - analyse_dataset_older_adults_flu_ethnicity_s1_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_s2_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_s3_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_s4_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_s5_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_s6_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_s7_specific_primary + - analyse_dataset_older_adults_flu_ses_s1_specific_primary + - analyse_dataset_older_adults_flu_ses_s2_specific_primary + - analyse_dataset_older_adults_flu_ses_s3_specific_primary + - analyse_dataset_older_adults_flu_ses_s4_specific_primary + - analyse_dataset_older_adults_flu_ses_s5_specific_primary + - analyse_dataset_older_adults_flu_ses_s6_specific_primary + - analyse_dataset_older_adults_flu_ses_s7_specific_primary + - analyse_dataset_older_adults_flu_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_flu_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_flu_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_flu_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_flu_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_flu_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_flu_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s1_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s2_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s3_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s4_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s5_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s6_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s7_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_flu_full_s1_specific_primary + - analyse_dataset_older_adults_flu_full_s2_specific_primary + - analyse_dataset_older_adults_flu_full_s3_specific_primary + - analyse_dataset_older_adults_flu_full_s4_specific_primary + - analyse_dataset_older_adults_flu_full_s5_specific_primary + - analyse_dataset_older_adults_flu_full_s6_specific_primary + - analyse_dataset_older_adults_flu_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/rates/rates_older_adults_2016_2017_sensitive.csv + glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv"): output/results/collated/older_adults_flu_model_outputs_collated.csv - analyse_dataset_older_adults_ethnicity_s1_sens: - run: r:latest analysis/ethnicity_models.R older_adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_older_adults_s1_sens] + collate_covid_model_outputs_tables_older_adults: + run: r:latest analysis/covid_model_outputs_table_collation.R older_adults older_adults + needs: + - analyse_dataset_older_adults_covid_ethnicity_s4_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_s5_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_s6_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_s7_specific_primary + - analyse_dataset_older_adults_covid_ses_s4_specific_primary + - analyse_dataset_older_adults_covid_ses_s5_specific_primary + - analyse_dataset_older_adults_covid_ses_s6_specific_primary + - analyse_dataset_older_adults_covid_ses_s7_specific_primary + - analyse_dataset_older_adults_covid_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_covid_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_covid_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_covid_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s4_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s5_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s6_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s7_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_covid_full_s4_specific_primary + - analyse_dataset_older_adults_covid_full_s5_specific_primary + - analyse_dataset_older_adults_covid_full_s6_specific_primary + - analyse_dataset_older_adults_covid_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_older_adults_2016_2017_sensitive.csv - - analyse_dataset_older_adults_ses_s1_sens: - run: r:latest analysis/ses_models.R older_adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_older_adults_s1_sens] + csv: output/results/collated/older_adults_covid_model_outputs_collated.csv + + collate_overall_and_all_cause_model_outputs_tables_older_adults: + run: r:latest analysis/overall_and_all_cause_model_outputs_table_collation.R older_adults + older_adults + needs: + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s1_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s2_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s3_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s4_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s5_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s6_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s7_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s1_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s2_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s3_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s4_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s5_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s6_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s7_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s1_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s2_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s3_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s4_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s5_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s6_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s7_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s1_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s2_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s3_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s4_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s5_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s6_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s7_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s1_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s2_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s3_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s4_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s5_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s6_specific_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_older_adults_2016_2017_sensitive.csv + csv: output/results/collated/older_adults_overall_and_all_cause_model_outputs_collated.csv - analyse_dataset_older_adults_hh_comp_s1_sens: - run: r:latest analysis/hh_comp_models.R older_adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_older_adults_s1_sens] + collate_rsv_sensitivity_model_outputs_tables_older_adults: + run: r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R older_adults + older_adults + needs: + - analyse_dataset_older_adults_rsv_ethnicity_s1_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_s2_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_s3_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_s4_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_s5_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_s6_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_s7_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_s1_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_s2_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_s3_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_s4_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_s5_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_s6_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_s7_sensitive_primary + - analyse_dataset_older_adults_rsv_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_rsv_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_rsv_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_rsv_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_rsv_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_rsv_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_rsv_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_rsv_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_rsv_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_rsv_full_s1_sensitive_primary + - analyse_dataset_older_adults_rsv_full_s2_sensitive_primary + - analyse_dataset_older_adults_rsv_full_s3_sensitive_primary + - analyse_dataset_older_adults_rsv_full_s4_sensitive_primary + - analyse_dataset_older_adults_rsv_full_s5_sensitive_primary + - analyse_dataset_older_adults_rsv_full_s6_sensitive_primary + - analyse_dataset_older_adults_rsv_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_older_adults_2016_2017_sensitive.csv + csv: output/results/collated/older_adults_rsv_sensitivity_model_outputs_collated.csv - generate_dataset_adults_s1_sens: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_adults_2016_2017_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow - -- adults season1_start_date season1_end_date sensitive primary + collate_flu_sensitivity_model_outputs_tables_older_adults: + run: r:latest analysis/flu_sensitivity_model_outputs_table_collation.R older_adults + older_adults + needs: + - analyse_dataset_older_adults_flu_ethnicity_s1_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_s2_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_s3_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_s4_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_s5_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_s6_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_s7_sensitive_primary + - analyse_dataset_older_adults_flu_ses_s1_sensitive_primary + - analyse_dataset_older_adults_flu_ses_s2_sensitive_primary + - analyse_dataset_older_adults_flu_ses_s3_sensitive_primary + - analyse_dataset_older_adults_flu_ses_s4_sensitive_primary + - analyse_dataset_older_adults_flu_ses_s5_sensitive_primary + - analyse_dataset_older_adults_flu_ses_s6_sensitive_primary + - analyse_dataset_older_adults_flu_ses_s7_sensitive_primary + - analyse_dataset_older_adults_flu_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_flu_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_flu_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_flu_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_flu_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_flu_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_flu_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_flu_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_flu_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_flu_full_s1_sensitive_primary + - analyse_dataset_older_adults_flu_full_s2_sensitive_primary + - analyse_dataset_older_adults_flu_full_s3_sensitive_primary + - analyse_dataset_older_adults_flu_full_s4_sensitive_primary + - analyse_dataset_older_adults_flu_full_s5_sensitive_primary + - analyse_dataset_older_adults_flu_full_s6_sensitive_primary + - analyse_dataset_older_adults_flu_full_s7_sensitive_primary outputs: - highly_sensitive: - dataset: output/data/input_adults_2016_2017_sensitive_primary.arrow + moderately_sensitive: + csv: output/results/collated/older_adults_flu_sensitivity_model_outputs_collated.csv - process_dataset_adults_s1_sens: - run: r:latest analysis/data_processing.R adults season1_start_date season1_end_date sensitive primary - needs: [generate_dataset_adults_s1_sens, process_household_information_s1] + collate_covid_sensitivity_model_outputs_tables_older_adults: + run: r:latest analysis/covid_sensitivity_model_outputs_table_collation.R older_adults + older_adults + needs: + - analyse_dataset_older_adults_covid_ethnicity_s4_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_s5_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_s6_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_s7_sensitive_primary + - analyse_dataset_older_adults_covid_ses_s4_sensitive_primary + - analyse_dataset_older_adults_covid_ses_s5_sensitive_primary + - analyse_dataset_older_adults_covid_ses_s6_sensitive_primary + - analyse_dataset_older_adults_covid_ses_s7_sensitive_primary + - analyse_dataset_older_adults_covid_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_covid_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_covid_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_covid_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_covid_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_covid_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_covid_full_s4_sensitive_primary + - analyse_dataset_older_adults_covid_full_s5_sensitive_primary + - analyse_dataset_older_adults_covid_full_s6_sensitive_primary + - analyse_dataset_older_adults_covid_full_s7_sensitive_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_adults_2016_2017_sensitive_primary.arrow + moderately_sensitive: + csv: output/results/collated/older_adults_covid_sensitivity_model_outputs_collated.csv - describe_dataset_adults_s1_sens: - run: r:latest analysis/report.R adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_adults_s1_sens] + collate_overall_and_all_cause_sensitivity_model_outputs_tables_older_adults: + run: r:latest analysis/overall_and_all_cause_sensitivity_model_outputs_table_collation.R + older_adults older_adults + needs: + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s1_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s2_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s3_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s4_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s5_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s6_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_s7_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s1_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s2_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s3_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s4_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s5_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s6_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_s7_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s1_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s2_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s3_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s4_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s5_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s6_sensitive_primary + - analyse_dataset_older_adults_overall_and_all_cause_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/rates/rates_adults_2016_2017_sensitive.csv + csv: output/results/collated/older_adults_overall_and_all_cause_sensitivity_model_outputs_collated.csv - analyse_dataset_adults_ethnicity_s1_sens: - run: r:latest analysis/ethnicity_models.R adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_adults_s1_sens] + collate_flow_chart_tables_adults: + run: r:latest analysis/flow_chart_table_collation.R adults adults + needs: + - process_flow_chart_data_adults_s1 + - process_flow_chart_data_adults_s2 + - process_flow_chart_data_adults_s3 + - process_flow_chart_data_adults_s4 + - process_flow_chart_data_adults_s5 + - process_flow_chart_data_adults_s6 + - process_flow_chart_data_adults_s7 outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_adults_2016_2017_sensitive.csv + csv: output/results/collated/adults_flow_chart_collated.csv - analyse_dataset_adults_ses_s1_sens: - run: r:latest analysis/ses_models.R adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_adults_s1_sens] + collate_table1_tables_adults: + run: r:latest analysis/table1_table_collation.R adults adults + needs: + - describe_dataset_adults_s1_specific_primary + - describe_dataset_adults_s2_specific_primary + - describe_dataset_adults_s3_specific_primary + - describe_dataset_adults_s4_specific_primary + - describe_dataset_adults_s5_specific_primary + - describe_dataset_adults_s6_specific_primary + - describe_dataset_adults_s7_specific_primary + - describe_dataset_adults_s1_sensitive_primary + - describe_dataset_adults_s2_sensitive_primary + - describe_dataset_adults_s3_sensitive_primary + - describe_dataset_adults_s4_sensitive_primary + - describe_dataset_adults_s5_sensitive_primary + - describe_dataset_adults_s6_sensitive_primary + - describe_dataset_adults_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_adults_2016_2017_sensitive.csv + csv: output/results/collated/adults_table1_collated.csv - analyse_dataset_adults_hh_comp_s1_sens: - run: r:latest analysis/hh_comp_models.R adults season1_start_date season1_end_date sensitive primary - needs: [process_dataset_adults_s1_sens] + collate_rates_tables_adults: + run: r:latest analysis/rates_table_collation.R adults adults + needs: + - process_dataset_adults_s1_specific_primary + - process_dataset_adults_s2_specific_primary + - process_dataset_adults_s3_specific_primary + - process_dataset_adults_s4_specific_primary + - process_dataset_adults_s5_specific_primary + - process_dataset_adults_s6_specific_primary + - process_dataset_adults_s7_specific_primary + - process_dataset_adults_s1_sensitive_primary + - process_dataset_adults_s2_sensitive_primary + - process_dataset_adults_s3_sensitive_primary + - process_dataset_adults_s4_sensitive_primary + - process_dataset_adults_s5_sensitive_primary + - process_dataset_adults_s6_sensitive_primary + - process_dataset_adults_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_adults_2016_2017_sensitive.csv + csv: output/results/collated/adults_rates_collated.csv - generate_dataset_children_and_adolescents_s1_sens: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2016_2017_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow - -- children_and_adolescents season1_start_date season1_end_date sensitive primary + collate_rsv_model_outputs_tables_adults: + run: r:latest analysis/rsv_model_outputs_table_collation.R adults adults + needs: + - analyse_dataset_adults_rsv_ethnicity_s1_specific_primary + - analyse_dataset_adults_rsv_ethnicity_s2_specific_primary + - analyse_dataset_adults_rsv_ethnicity_s3_specific_primary + - analyse_dataset_adults_rsv_ethnicity_s4_specific_primary + - analyse_dataset_adults_rsv_ethnicity_s5_specific_primary + - analyse_dataset_adults_rsv_ethnicity_s6_specific_primary + - analyse_dataset_adults_rsv_ethnicity_s7_specific_primary + - analyse_dataset_adults_rsv_ses_s1_specific_primary + - analyse_dataset_adults_rsv_ses_s2_specific_primary + - analyse_dataset_adults_rsv_ses_s3_specific_primary + - analyse_dataset_adults_rsv_ses_s4_specific_primary + - analyse_dataset_adults_rsv_ses_s5_specific_primary + - analyse_dataset_adults_rsv_ses_s6_specific_primary + - analyse_dataset_adults_rsv_ses_s7_specific_primary + - analyse_dataset_adults_rsv_hh_comp_s1_specific_primary + - analyse_dataset_adults_rsv_hh_comp_s2_specific_primary + - analyse_dataset_adults_rsv_hh_comp_s3_specific_primary + - analyse_dataset_adults_rsv_hh_comp_s4_specific_primary + - analyse_dataset_adults_rsv_hh_comp_s5_specific_primary + - analyse_dataset_adults_rsv_hh_comp_s6_specific_primary + - analyse_dataset_adults_rsv_hh_comp_s7_specific_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s1_specific_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s2_specific_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s3_specific_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s4_specific_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s5_specific_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s6_specific_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s7_specific_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s1_specific_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s2_specific_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s3_specific_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s4_specific_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s5_specific_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s6_specific_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s7_specific_primary + - analyse_dataset_adults_rsv_full_s1_specific_primary + - analyse_dataset_adults_rsv_full_s2_specific_primary + - analyse_dataset_adults_rsv_full_s3_specific_primary + - analyse_dataset_adults_rsv_full_s4_specific_primary + - analyse_dataset_adults_rsv_full_s5_specific_primary + - analyse_dataset_adults_rsv_full_s6_specific_primary + - analyse_dataset_adults_rsv_full_s7_specific_primary outputs: - highly_sensitive: - dataset: output/data/input_children_and_adolescents_2016_2017_sensitive_primary.arrow + moderately_sensitive: + csv: output/results/collated/adults_rsv_model_outputs_collated.csv - process_dataset_children_and_adolescents_s1_sens: - run: r:latest analysis/data_processing.R children_and_adolescents season1_start_date season1_end_date sensitive primary - needs: [generate_dataset_children_and_adolescents_s1_sens, process_household_information_s1] + collate_flu_model_outputs_tables_adults: + run: r:latest analysis/flu_model_outputs_table_collation.R adults adults + needs: + - analyse_dataset_adults_flu_ethnicity_s1_specific_primary + - analyse_dataset_adults_flu_ethnicity_s2_specific_primary + - analyse_dataset_adults_flu_ethnicity_s3_specific_primary + - analyse_dataset_adults_flu_ethnicity_s4_specific_primary + - analyse_dataset_adults_flu_ethnicity_s5_specific_primary + - analyse_dataset_adults_flu_ethnicity_s6_specific_primary + - analyse_dataset_adults_flu_ethnicity_s7_specific_primary + - analyse_dataset_adults_flu_ses_s1_specific_primary + - analyse_dataset_adults_flu_ses_s2_specific_primary + - analyse_dataset_adults_flu_ses_s3_specific_primary + - analyse_dataset_adults_flu_ses_s4_specific_primary + - analyse_dataset_adults_flu_ses_s5_specific_primary + - analyse_dataset_adults_flu_ses_s6_specific_primary + - analyse_dataset_adults_flu_ses_s7_specific_primary + - analyse_dataset_adults_flu_hh_comp_s1_specific_primary + - analyse_dataset_adults_flu_hh_comp_s2_specific_primary + - analyse_dataset_adults_flu_hh_comp_s3_specific_primary + - analyse_dataset_adults_flu_hh_comp_s4_specific_primary + - analyse_dataset_adults_flu_hh_comp_s5_specific_primary + - analyse_dataset_adults_flu_hh_comp_s6_specific_primary + - analyse_dataset_adults_flu_hh_comp_s7_specific_primary + - analyse_dataset_adults_flu_ethnicity_ses_s1_specific_primary + - analyse_dataset_adults_flu_ethnicity_ses_s2_specific_primary + - analyse_dataset_adults_flu_ethnicity_ses_s3_specific_primary + - analyse_dataset_adults_flu_ethnicity_ses_s4_specific_primary + - analyse_dataset_adults_flu_ethnicity_ses_s5_specific_primary + - analyse_dataset_adults_flu_ethnicity_ses_s6_specific_primary + - analyse_dataset_adults_flu_ethnicity_ses_s7_specific_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_adults_flu_ses_hh_comp_s1_specific_primary + - analyse_dataset_adults_flu_ses_hh_comp_s2_specific_primary + - analyse_dataset_adults_flu_ses_hh_comp_s3_specific_primary + - analyse_dataset_adults_flu_ses_hh_comp_s4_specific_primary + - analyse_dataset_adults_flu_ses_hh_comp_s5_specific_primary + - analyse_dataset_adults_flu_ses_hh_comp_s6_specific_primary + - analyse_dataset_adults_flu_ses_hh_comp_s7_specific_primary + - analyse_dataset_adults_flu_full_s1_specific_primary + - analyse_dataset_adults_flu_full_s2_specific_primary + - analyse_dataset_adults_flu_full_s3_specific_primary + - analyse_dataset_adults_flu_full_s4_specific_primary + - analyse_dataset_adults_flu_full_s5_specific_primary + - analyse_dataset_adults_flu_full_s6_specific_primary + - analyse_dataset_adults_flu_full_s7_specific_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2016_2017_sensitive_primary.arrow + moderately_sensitive: + glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv"): output/results/collated/adults_flu_model_outputs_collated.csv - describe_dataset_children_and_adolescents_s1_sens: - run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date sensitive primary - needs: [process_dataset_children_and_adolescents_s1_sens] + collate_covid_model_outputs_tables_adults: + run: r:latest analysis/covid_model_outputs_table_collation.R adults adults + needs: + - analyse_dataset_adults_covid_ethnicity_s4_specific_primary + - analyse_dataset_adults_covid_ethnicity_s5_specific_primary + - analyse_dataset_adults_covid_ethnicity_s6_specific_primary + - analyse_dataset_adults_covid_ethnicity_s7_specific_primary + - analyse_dataset_adults_covid_ses_s4_specific_primary + - analyse_dataset_adults_covid_ses_s5_specific_primary + - analyse_dataset_adults_covid_ses_s6_specific_primary + - analyse_dataset_adults_covid_ses_s7_specific_primary + - analyse_dataset_adults_covid_hh_comp_s4_specific_primary + - analyse_dataset_adults_covid_hh_comp_s5_specific_primary + - analyse_dataset_adults_covid_hh_comp_s6_specific_primary + - analyse_dataset_adults_covid_hh_comp_s7_specific_primary + - analyse_dataset_adults_covid_ethnicity_ses_s4_specific_primary + - analyse_dataset_adults_covid_ethnicity_ses_s5_specific_primary + - analyse_dataset_adults_covid_ethnicity_ses_s6_specific_primary + - analyse_dataset_adults_covid_ethnicity_ses_s7_specific_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_adults_covid_ses_hh_comp_s4_specific_primary + - analyse_dataset_adults_covid_ses_hh_comp_s5_specific_primary + - analyse_dataset_adults_covid_ses_hh_comp_s6_specific_primary + - analyse_dataset_adults_covid_ses_hh_comp_s7_specific_primary + - analyse_dataset_adults_covid_full_s4_specific_primary + - analyse_dataset_adults_covid_full_s5_specific_primary + - analyse_dataset_adults_covid_full_s6_specific_primary + - analyse_dataset_adults_covid_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2016_2017_sensitive.csv + csv: output/results/collated/adults_covid_model_outputs_collated.csv - analyse_dataset_children_and_adolescents_ethnicity_s1_sens: - run: r:latest analysis/ethnicity_models.R children_and_adolescents season1_start_date season1_end_date sensitive primary - needs: [process_dataset_children_and_adolescents_s1_sens] + collate_overall_and_all_cause_model_outputs_tables_adults: + run: r:latest analysis/overall_and_all_cause_model_outputs_table_collation.R adults + adults + needs: + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s1_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s2_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s3_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s4_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s5_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s6_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s7_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s1_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s2_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s3_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s4_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s5_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s6_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s7_specific_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s1_specific_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s2_specific_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s3_specific_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s4_specific_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s5_specific_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s6_specific_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s7_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s1_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s2_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s3_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s4_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s5_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s6_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s7_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s1_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s2_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s3_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s4_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s5_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s6_specific_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s7_specific_primary + - analyse_dataset_adults_overall_and_all_cause_full_s1_specific_primary + - analyse_dataset_adults_overall_and_all_cause_full_s2_specific_primary + - analyse_dataset_adults_overall_and_all_cause_full_s3_specific_primary + - analyse_dataset_adults_overall_and_all_cause_full_s4_specific_primary + - analyse_dataset_adults_overall_and_all_cause_full_s5_specific_primary + - analyse_dataset_adults_overall_and_all_cause_full_s6_specific_primary + - analyse_dataset_adults_overall_and_all_cause_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_children_and_adolescents_2016_2017_sensitive.csv + csv: output/results/collated/adults_overall_and_all_cause_model_outputs_collated.csv - analyse_dataset_children_and_adolescents_ses_s1_sens: - run: r:latest analysis/ses_models.R children_and_adolescents season1_start_date season1_end_date sensitive primary - needs: [process_dataset_children_and_adolescents_s1_sens] + collate_rsv_sensitivity_model_outputs_tables_adults: + run: r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R adults + adults + needs: + - analyse_dataset_adults_rsv_ethnicity_s1_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_s2_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_s3_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_s4_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_s5_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_s6_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_s7_sensitive_primary + - analyse_dataset_adults_rsv_ses_s1_sensitive_primary + - analyse_dataset_adults_rsv_ses_s2_sensitive_primary + - analyse_dataset_adults_rsv_ses_s3_sensitive_primary + - analyse_dataset_adults_rsv_ses_s4_sensitive_primary + - analyse_dataset_adults_rsv_ses_s5_sensitive_primary + - analyse_dataset_adults_rsv_ses_s6_sensitive_primary + - analyse_dataset_adults_rsv_ses_s7_sensitive_primary + - analyse_dataset_adults_rsv_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_rsv_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_rsv_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_rsv_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_rsv_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_rsv_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_rsv_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_rsv_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_rsv_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_rsv_full_s1_sensitive_primary + - analyse_dataset_adults_rsv_full_s2_sensitive_primary + - analyse_dataset_adults_rsv_full_s3_sensitive_primary + - analyse_dataset_adults_rsv_full_s4_sensitive_primary + - analyse_dataset_adults_rsv_full_s5_sensitive_primary + - analyse_dataset_adults_rsv_full_s6_sensitive_primary + - analyse_dataset_adults_rsv_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/ses_model_outputs_children_and_adolescents_2016_2017_sensitive.csv + csv: output/results/collated/adults_rsv_sensitivity_model_outputs_collated.csv - analyse_dataset_children_and_adolescents_hh_comp_s1_sens: - run: r:latest analysis/hh_comp_models.R children_and_adolescents season1_start_date season1_end_date sensitive primary - needs: [process_dataset_children_and_adolescents_s1_sens] + collate_flu_sensitivity_model_outputs_tables_adults: + run: r:latest analysis/flu_sensitivity_model_outputs_table_collation.R adults + adults + needs: + - analyse_dataset_adults_flu_ethnicity_s1_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_s2_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_s3_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_s4_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_s5_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_s6_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_s7_sensitive_primary + - analyse_dataset_adults_flu_ses_s1_sensitive_primary + - analyse_dataset_adults_flu_ses_s2_sensitive_primary + - analyse_dataset_adults_flu_ses_s3_sensitive_primary + - analyse_dataset_adults_flu_ses_s4_sensitive_primary + - analyse_dataset_adults_flu_ses_s5_sensitive_primary + - analyse_dataset_adults_flu_ses_s6_sensitive_primary + - analyse_dataset_adults_flu_ses_s7_sensitive_primary + - analyse_dataset_adults_flu_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_flu_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_flu_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_flu_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_flu_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_flu_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_flu_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_flu_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_flu_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_flu_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_flu_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_flu_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_flu_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_flu_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_flu_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_flu_full_s1_sensitive_primary + - analyse_dataset_adults_flu_full_s2_sensitive_primary + - analyse_dataset_adults_flu_full_s3_sensitive_primary + - analyse_dataset_adults_flu_full_s4_sensitive_primary + - analyse_dataset_adults_flu_full_s5_sensitive_primary + - analyse_dataset_adults_flu_full_s6_sensitive_primary + - analyse_dataset_adults_flu_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/hh_comp_model_outputs_children_and_adolescents_2016_2017_sensitive.csv + csv: output/results/collated/adults_flu_sensitivity_model_outputs_collated.csv - generate_dataset_infants_s1_sens: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2016_2017_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow - -- infants season1_start_date season1_end_date sensitive primary + collate_covid_sensitivity_model_outputs_tables_adults: + run: r:latest analysis/covid_sensitivity_model_outputs_table_collation.R adults + adults + needs: + - analyse_dataset_adults_covid_ethnicity_s4_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_s5_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_s6_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_s7_sensitive_primary + - analyse_dataset_adults_covid_ses_s4_sensitive_primary + - analyse_dataset_adults_covid_ses_s5_sensitive_primary + - analyse_dataset_adults_covid_ses_s6_sensitive_primary + - analyse_dataset_adults_covid_ses_s7_sensitive_primary + - analyse_dataset_adults_covid_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_covid_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_covid_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_covid_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_covid_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_covid_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_covid_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_covid_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_covid_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_covid_full_s4_sensitive_primary + - analyse_dataset_adults_covid_full_s5_sensitive_primary + - analyse_dataset_adults_covid_full_s6_sensitive_primary + - analyse_dataset_adults_covid_full_s7_sensitive_primary outputs: - highly_sensitive: - dataset: output/data/input_infants_2016_2017_sensitive_primary.arrow + moderately_sensitive: + csv: output/results/collated/adults_covid_sensitivity_model_outputs_collated.csv - process_dataset_infants_s1_sens: - run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date sensitive primary - needs: [generate_dataset_infants_s1_sens, process_household_information_s1] + collate_overall_and_all_cause_sensitivity_model_outputs_tables_adults: + run: r:latest analysis/overall_and_all_cause_sensitivity_model_outputs_table_collation.R + adults adults + needs: + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s1_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s2_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s3_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s4_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s5_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s6_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_s7_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s1_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s2_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s3_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s4_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s5_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s6_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_s7_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_full_s1_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_full_s2_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_full_s3_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_full_s4_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_full_s5_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_full_s6_sensitive_primary + - analyse_dataset_adults_overall_and_all_cause_full_s7_sensitive_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2016_2017_sensitive_primary.arrow + moderately_sensitive: + csv: output/results/collated/adults_overall_and_all_cause_sensitivity_model_outputs_collated.csv - describe_dataset_infants_s1_sens: - run: r:latest analysis/report.R infants season1_start_date season1_end_date sensitive primary - needs: [process_dataset_infants_s1_sens] + collate_flow_chart_tables_children_and_adolescents: + run: r:latest analysis/flow_chart_table_collation.R children_and_adolescents children_and_adolescents + needs: + - process_flow_chart_data_children_and_adolescents_s1 + - process_flow_chart_data_children_and_adolescents_s2 + - process_flow_chart_data_children_and_adolescents_s3 + - process_flow_chart_data_children_and_adolescents_s4 + - process_flow_chart_data_children_and_adolescents_s5 + - process_flow_chart_data_children_and_adolescents_s6 + - process_flow_chart_data_children_and_adolescents_s7 outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2016_2017_sensitive.csv + csv: output/results/collated/children_and_adolescents_flow_chart_collated.csv - analyse_dataset_infants_ethnicity_s1_sens: - run: r:latest analysis/ethnicity_models.R infants season1_start_date season1_end_date sensitive primary - needs: [process_dataset_infants_s1_sens] + collate_table1_tables_children_and_adolescents: + run: r:latest analysis/table1_table_collation.R children_and_adolescents children_and_adolescents + needs: + - describe_dataset_children_and_adolescents_s1_specific_primary + - describe_dataset_children_and_adolescents_s2_specific_primary + - describe_dataset_children_and_adolescents_s3_specific_primary + - describe_dataset_children_and_adolescents_s4_specific_primary + - describe_dataset_children_and_adolescents_s5_specific_primary + - describe_dataset_children_and_adolescents_s6_specific_primary + - describe_dataset_children_and_adolescents_s7_specific_primary + - describe_dataset_children_and_adolescents_s1_sensitive_primary + - describe_dataset_children_and_adolescents_s2_sensitive_primary + - describe_dataset_children_and_adolescents_s3_sensitive_primary + - describe_dataset_children_and_adolescents_s4_sensitive_primary + - describe_dataset_children_and_adolescents_s5_sensitive_primary + - describe_dataset_children_and_adolescents_s6_sensitive_primary + - describe_dataset_children_and_adolescents_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/ethnicity_model_outputs_infants_2016_2017_sensitive.csv + csv: output/results/collated/children_and_adolescents_table1_collated.csv -### secondary analysis + collate_rates_tables_children_and_adolescents: + run: r:latest analysis/rates_table_collation.R children_and_adolescents children_and_adolescents + needs: + - process_dataset_children_and_adolescents_s1_specific_primary + - process_dataset_children_and_adolescents_s2_specific_primary + - process_dataset_children_and_adolescents_s3_specific_primary + - process_dataset_children_and_adolescents_s4_specific_primary + - process_dataset_children_and_adolescents_s5_specific_primary + - process_dataset_children_and_adolescents_s6_specific_primary + - process_dataset_children_and_adolescents_s7_specific_primary + - process_dataset_children_and_adolescents_s1_sensitive_primary + - process_dataset_children_and_adolescents_s2_sensitive_primary + - process_dataset_children_and_adolescents_s3_sensitive_primary + - process_dataset_children_and_adolescents_s4_sensitive_primary + - process_dataset_children_and_adolescents_s5_sensitive_primary + - process_dataset_children_and_adolescents_s6_sensitive_primary + - process_dataset_children_and_adolescents_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_rates_collated.csv -## season 1 (2016/17) + collate_rsv_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/rsv_model_outputs_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s1_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s2_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s3_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s4_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s5_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s6_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s7_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s1_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s2_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s3_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s1_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s2_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s3_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_rsv_full_s1_specific_primary + - analyse_dataset_children_and_adolescents_rsv_full_s2_specific_primary + - analyse_dataset_children_and_adolescents_rsv_full_s3_specific_primary + - analyse_dataset_children_and_adolescents_rsv_full_s4_specific_primary + - analyse_dataset_children_and_adolescents_rsv_full_s5_specific_primary + - analyse_dataset_children_and_adolescents_rsv_full_s6_specific_primary + - analyse_dataset_children_and_adolescents_rsv_full_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_rsv_model_outputs_collated.csv - generate_dataset_older_adults_s1_sens_sec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_older_adults_2016_2017_sensitive_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_older_adults_2016_2017.arrow - -- older_adults season1_start_date season1_end_date sensitive secondary + collate_flu_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/flu_model_outputs_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_flu_ethnicity_s1_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s2_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s3_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s4_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s5_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s6_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s7_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_s1_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_s2_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_s3_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s1_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s2_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s3_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_flu_full_s1_specific_primary + - analyse_dataset_children_and_adolescents_flu_full_s2_specific_primary + - analyse_dataset_children_and_adolescents_flu_full_s3_specific_primary + - analyse_dataset_children_and_adolescents_flu_full_s4_specific_primary + - analyse_dataset_children_and_adolescents_flu_full_s5_specific_primary + - analyse_dataset_children_and_adolescents_flu_full_s6_specific_primary + - analyse_dataset_children_and_adolescents_flu_full_s7_specific_primary outputs: - highly_sensitive: - dataset: output/data/input_older_adults_2016_2017_sensitive_secondary.arrow + moderately_sensitive: + glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv"): output/results/collated/children_and_adolescents_flu_model_outputs_collated.csv - process_dataset_older_adults_s1_sens_sec: - run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date sensitive secondary - needs: [generate_dataset_older_adults_s1_sens_sec, process_household_information_s1] + collate_covid_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/covid_model_outputs_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_covid_ethnicity_s4_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_s5_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_s6_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_s7_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_covid_full_s4_specific_primary + - analyse_dataset_children_and_adolescents_covid_full_s5_specific_primary + - analyse_dataset_children_and_adolescents_covid_full_s6_specific_primary + - analyse_dataset_children_and_adolescents_covid_full_s7_specific_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_older_adults_2016_2017_sensitive_secondary.arrow - - generate_dataset_adults_s1_sens_sec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_adults_2016_2017_sensitive_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_adults_2016_2017.arrow - -- adults season1_start_date season1_end_date sensitive secondary + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_covid_model_outputs_collated.csv + + collate_overall_and_all_cause_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/overall_and_all_cause_model_outputs_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s1_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s2_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s3_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s4_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s5_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s6_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s7_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s1_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s2_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s3_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s1_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s2_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s3_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s4_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s5_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s6_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s7_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s1_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s2_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s3_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s4_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s5_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s6_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s7_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s1_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s2_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s3_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s4_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s5_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s6_specific_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s7_specific_primary outputs: - highly_sensitive: - dataset: output/data/input_adults_2016_2017_sensitive_secondary.arrow + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_overall_and_all_cause_model_outputs_collated.csv - process_dataset_adults_s1_sens_sec: - run: r:latest analysis/data_processing.R adults season1_start_date season1_end_date sensitive secondary - needs: [generate_dataset_adults_s1_sens_sec, process_household_information_s1] + collate_rsv_sensitivity_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_full_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_full_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_full_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_full_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_full_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_full_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_rsv_full_s7_sensitive_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_adults_2016_2017_sensitive_secondary.arrow - - generate_dataset_children_and_adolescents_s1_sens_sec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2016_2017_sensitive_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2016_2017.arrow - -- children_and_adolescents season1_start_date season1_end_date sensitive secondary + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_rsv_sensitivity_model_outputs_collated.csv + + collate_flu_sensitivity_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/flu_sensitivity_model_outputs_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_flu_ethnicity_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_full_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_full_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_full_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_full_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_full_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_full_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_flu_full_s7_sensitive_primary outputs: - highly_sensitive: - dataset: output/data/input_children_and_adolescents_2016_2017_sensitive_secondary.arrow + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_flu_sensitivity_model_outputs_collated.csv - process_dataset_children_and_adolescents_s1_sens_sec: - run: r:latest analysis/data_processing.R children_and_adolescents season1_start_date season1_end_date sensitive secondary - needs: [generate_dataset_children_and_adolescents_s1_sens_sec, process_household_information_s1] + collate_covid_sensitivity_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/covid_sensitivity_model_outputs_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_covid_ethnicity_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_full_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_full_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_full_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_covid_full_s7_sensitive_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2016_2017_sensitive_secondary.arrow - - generate_dataset_infants_s1_sens_sec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2016_2017_sensitive_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow - -- infants season1_start_date season1_end_date sensitive secondary + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_covid_sensitivity_model_outputs_collated.csv + + collate_overall_and_all_cause_sensitivity_model_outputs_tables_children_and_adolescents: + run: r:latest analysis/overall_and_all_cause_sensitivity_model_outputs_table_collation.R + children_and_adolescents children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s1_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s2_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s3_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s4_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s5_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s6_sensitive_primary + - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s7_sensitive_primary outputs: - highly_sensitive: - dataset: output/data/input_infants_2016_2017_sensitive_secondary.arrow + moderately_sensitive: + csv: output/results/collated/children_and_adolescents_overall_and_all_cause_sensitivity_model_outputs_collated.csv - process_dataset_infants_s1_sens_sec: - run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date sensitive secondary - needs: [generate_dataset_infants_s1_sens_sec, process_household_information_s1] + collate_flow_chart_tables_infants: + run: r:latest analysis/flow_chart_table_collation.R infants infants + needs: + - process_flow_chart_data_infants_s1 + - process_flow_chart_data_infants_s2 + - process_flow_chart_data_infants_s3 + - process_flow_chart_data_infants_s4 + - process_flow_chart_data_infants_s5 + - process_flow_chart_data_infants_s6 + - process_flow_chart_data_infants_s7 outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2016_2017_sensitive_secondary.arrow + moderately_sensitive: + csv: output/results/collated/infants_flow_chart_collated.csv -## season 7 (2022/23) + collate_table1_tables_infants: + run: r:latest analysis/table1_table_collation.R infants infants + needs: + - describe_dataset_infants_s1_specific_primary + - describe_dataset_infants_s2_specific_primary + - describe_dataset_infants_s3_specific_primary + - describe_dataset_infants_s4_specific_primary + - describe_dataset_infants_s5_specific_primary + - describe_dataset_infants_s6_specific_primary + - describe_dataset_infants_s7_specific_primary + - describe_dataset_infants_s1_sensitive_primary + - describe_dataset_infants_s2_sensitive_primary + - describe_dataset_infants_s3_sensitive_primary + - describe_dataset_infants_s4_sensitive_primary + - describe_dataset_infants_s5_sensitive_primary + - describe_dataset_infants_s6_sensitive_primary + - describe_dataset_infants_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/collated/infants_table1_collated.csv - generate_dataset_adults_s7_sens_sec: - run: > - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_adults_2022_2023_sensitive_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow - -- adults season7_start_date season7_end_date sensitive secondary + collate_rates_tables_infants: + run: r:latest analysis/rates_table_collation.R infants infants + needs: + - process_dataset_infants_s1_specific_primary + - process_dataset_infants_s2_specific_primary + - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary + - process_dataset_infants_s5_specific_primary + - process_dataset_infants_s6_specific_primary + - process_dataset_infants_s7_specific_primary + - process_dataset_infants_s1_sensitive_primary + - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary + - process_dataset_infants_s4_sensitive_primary + - process_dataset_infants_s5_sensitive_primary + - process_dataset_infants_s6_sensitive_primary + - process_dataset_infants_s7_sensitive_primary outputs: - highly_sensitive: - dataset: output/data/input_adults_2022_2023_sensitive_secondary.arrow + moderately_sensitive: + csv: output/results/collated/infants_rates_collated.csv - process_dataset_adults_s7_sens_sec: - run: r:latest analysis/data_processing.R adults season7_start_date season7_end_date sensitive secondary - needs: [generate_dataset_adults_s7_sens_sec, process_household_information_s7] + collate_rsv_model_outputs_tables_infants: + run: r:latest analysis/rsv_model_outputs_table_collation.R infants infants + needs: + - analyse_dataset_infants_rsv_ethnicity_s1_specific_primary + - analyse_dataset_infants_rsv_ethnicity_s2_specific_primary + - analyse_dataset_infants_rsv_ethnicity_s3_specific_primary + - analyse_dataset_infants_rsv_ethnicity_s4_specific_primary + - analyse_dataset_infants_rsv_ethnicity_s5_specific_primary + - analyse_dataset_infants_rsv_ethnicity_s6_specific_primary + - analyse_dataset_infants_rsv_ethnicity_s7_specific_primary + - analyse_dataset_infants_rsv_ses_s1_specific_primary + - analyse_dataset_infants_rsv_ses_s2_specific_primary + - analyse_dataset_infants_rsv_ses_s3_specific_primary + - analyse_dataset_infants_rsv_ses_s4_specific_primary + - analyse_dataset_infants_rsv_ses_s5_specific_primary + - analyse_dataset_infants_rsv_ses_s6_specific_primary + - analyse_dataset_infants_rsv_ses_s7_specific_primary + - analyse_dataset_infants_rsv_hh_comp_s1_specific_primary + - analyse_dataset_infants_rsv_hh_comp_s2_specific_primary + - analyse_dataset_infants_rsv_hh_comp_s3_specific_primary + - analyse_dataset_infants_rsv_hh_comp_s4_specific_primary + - analyse_dataset_infants_rsv_hh_comp_s5_specific_primary + - analyse_dataset_infants_rsv_hh_comp_s6_specific_primary + - analyse_dataset_infants_rsv_hh_comp_s7_specific_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s1_specific_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s2_specific_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s3_specific_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s4_specific_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s5_specific_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s6_specific_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s7_specific_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s1_specific_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s2_specific_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s3_specific_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s4_specific_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s5_specific_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s6_specific_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s7_specific_primary + - analyse_dataset_infants_rsv_full_s1_specific_primary + - analyse_dataset_infants_rsv_full_s2_specific_primary + - analyse_dataset_infants_rsv_full_s3_specific_primary + - analyse_dataset_infants_rsv_full_s4_specific_primary + - analyse_dataset_infants_rsv_full_s5_specific_primary + - analyse_dataset_infants_rsv_full_s6_specific_primary + - analyse_dataset_infants_rsv_full_s7_specific_primary outputs: - highly_sensitive: - cohort: output/data/input_processed_adults_2022_2023_sensitive_secondary.arrow + moderately_sensitive: + csv: output/results/collated/infants_rsv_model_outputs_collated.csv -## season 1 (2016/17) - cohort description + collate_flu_model_outputs_tables_infants: + run: r:latest analysis/flu_model_outputs_table_collation.R infants infants + needs: + - analyse_dataset_infants_flu_ethnicity_s1_specific_primary + - analyse_dataset_infants_flu_ethnicity_s2_specific_primary + - analyse_dataset_infants_flu_ethnicity_s3_specific_primary + - analyse_dataset_infants_flu_ethnicity_s4_specific_primary + - analyse_dataset_infants_flu_ethnicity_s5_specific_primary + - analyse_dataset_infants_flu_ethnicity_s6_specific_primary + - analyse_dataset_infants_flu_ethnicity_s7_specific_primary + - analyse_dataset_infants_flu_ses_s1_specific_primary + - analyse_dataset_infants_flu_ses_s2_specific_primary + - analyse_dataset_infants_flu_ses_s3_specific_primary + - analyse_dataset_infants_flu_ses_s4_specific_primary + - analyse_dataset_infants_flu_ses_s5_specific_primary + - analyse_dataset_infants_flu_ses_s6_specific_primary + - analyse_dataset_infants_flu_ses_s7_specific_primary + - analyse_dataset_infants_flu_hh_comp_s1_specific_primary + - analyse_dataset_infants_flu_hh_comp_s2_specific_primary + - analyse_dataset_infants_flu_hh_comp_s3_specific_primary + - analyse_dataset_infants_flu_hh_comp_s4_specific_primary + - analyse_dataset_infants_flu_hh_comp_s5_specific_primary + - analyse_dataset_infants_flu_hh_comp_s6_specific_primary + - analyse_dataset_infants_flu_hh_comp_s7_specific_primary + - analyse_dataset_infants_flu_ethnicity_ses_s1_specific_primary + - analyse_dataset_infants_flu_ethnicity_ses_s2_specific_primary + - analyse_dataset_infants_flu_ethnicity_ses_s3_specific_primary + - analyse_dataset_infants_flu_ethnicity_ses_s4_specific_primary + - analyse_dataset_infants_flu_ethnicity_ses_s5_specific_primary + - analyse_dataset_infants_flu_ethnicity_ses_s6_specific_primary + - analyse_dataset_infants_flu_ethnicity_ses_s7_specific_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_infants_flu_ses_hh_comp_s1_specific_primary + - analyse_dataset_infants_flu_ses_hh_comp_s2_specific_primary + - analyse_dataset_infants_flu_ses_hh_comp_s3_specific_primary + - analyse_dataset_infants_flu_ses_hh_comp_s4_specific_primary + - analyse_dataset_infants_flu_ses_hh_comp_s5_specific_primary + - analyse_dataset_infants_flu_ses_hh_comp_s6_specific_primary + - analyse_dataset_infants_flu_ses_hh_comp_s7_specific_primary + - analyse_dataset_infants_flu_full_s1_specific_primary + - analyse_dataset_infants_flu_full_s2_specific_primary + - analyse_dataset_infants_flu_full_s3_specific_primary + - analyse_dataset_infants_flu_full_s4_specific_primary + - analyse_dataset_infants_flu_full_s5_specific_primary + - analyse_dataset_infants_flu_full_s6_specific_primary + - analyse_dataset_infants_flu_full_s7_specific_primary + outputs: + moderately_sensitive: + glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv"): output/results/collated/infants_flu_model_outputs_collated.csv - describe_cohort_older_adults_s1: - run: r:latest analysis/cohort_description.R older_adults season1_start_date season1_end_date sensitive secondary - needs: [process_dataset_older_adults_s1_sens_sec] + collate_covid_model_outputs_tables_infants: + run: r:latest analysis/covid_model_outputs_table_collation.R infants infants + needs: + - analyse_dataset_infants_covid_ethnicity_s4_specific_primary + - analyse_dataset_infants_covid_ethnicity_s5_specific_primary + - analyse_dataset_infants_covid_ethnicity_s6_specific_primary + - analyse_dataset_infants_covid_ethnicity_s7_specific_primary + - analyse_dataset_infants_covid_ses_s4_specific_primary + - analyse_dataset_infants_covid_ses_s5_specific_primary + - analyse_dataset_infants_covid_ses_s6_specific_primary + - analyse_dataset_infants_covid_ses_s7_specific_primary + - analyse_dataset_infants_covid_hh_comp_s4_specific_primary + - analyse_dataset_infants_covid_hh_comp_s5_specific_primary + - analyse_dataset_infants_covid_hh_comp_s6_specific_primary + - analyse_dataset_infants_covid_hh_comp_s7_specific_primary + - analyse_dataset_infants_covid_ethnicity_ses_s4_specific_primary + - analyse_dataset_infants_covid_ethnicity_ses_s5_specific_primary + - analyse_dataset_infants_covid_ethnicity_ses_s6_specific_primary + - analyse_dataset_infants_covid_ethnicity_ses_s7_specific_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_infants_covid_ses_hh_comp_s4_specific_primary + - analyse_dataset_infants_covid_ses_hh_comp_s5_specific_primary + - analyse_dataset_infants_covid_ses_hh_comp_s6_specific_primary + - analyse_dataset_infants_covid_ses_hh_comp_s7_specific_primary + - analyse_dataset_infants_covid_full_s4_specific_primary + - analyse_dataset_infants_covid_full_s5_specific_primary + - analyse_dataset_infants_covid_full_s6_specific_primary + - analyse_dataset_infants_covid_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2016_2017.csv + csv: output/results/collated/infants_covid_model_outputs_collated.csv - describe_cohort_adults_s1: - run: r:latest analysis/cohort_description.R adults season1_start_date season1_end_date sensitive secondary - needs: [process_dataset_adults_s1_sens_sec] + collate_overall_and_all_cause_model_outputs_tables_infants: + run: r:latest analysis/overall_and_all_cause_model_outputs_table_collation.R infants + infants + needs: + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s2_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s6_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s7_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s1_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s2_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s3_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s4_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s5_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s6_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s7_specific_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s1_specific_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s2_specific_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_specific_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s4_specific_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_specific_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s6_specific_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s7_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s1_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s2_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s4_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s6_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s7_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s1_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s2_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s6_specific_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s7_specific_primary + - analyse_dataset_infants_overall_and_all_cause_full_s1_specific_primary + - analyse_dataset_infants_overall_and_all_cause_full_s2_specific_primary + - analyse_dataset_infants_overall_and_all_cause_full_s3_specific_primary + - analyse_dataset_infants_overall_and_all_cause_full_s4_specific_primary + - analyse_dataset_infants_overall_and_all_cause_full_s5_specific_primary + - analyse_dataset_infants_overall_and_all_cause_full_s6_specific_primary + - analyse_dataset_infants_overall_and_all_cause_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2016_2017.csv + csv: output/results/collated/infants_overall_and_all_cause_model_outputs_collated.csv - describe_cohort_children_and_adolescents_s1: - run: r:latest analysis/cohort_description.R children_and_adolescents season1_start_date season1_end_date sensitive secondary - needs: [process_dataset_children_and_adolescents_s1_sens_sec] + collate_rsv_sensitivity_model_outputs_tables_infants: + run: r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R infants + infants + needs: + - analyse_dataset_infants_rsv_ethnicity_s1_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_s2_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_s3_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_s4_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_s5_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_s6_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_s7_sensitive_primary + - analyse_dataset_infants_rsv_ses_s1_sensitive_primary + - analyse_dataset_infants_rsv_ses_s2_sensitive_primary + - analyse_dataset_infants_rsv_ses_s3_sensitive_primary + - analyse_dataset_infants_rsv_ses_s4_sensitive_primary + - analyse_dataset_infants_rsv_ses_s5_sensitive_primary + - analyse_dataset_infants_rsv_ses_s6_sensitive_primary + - analyse_dataset_infants_rsv_ses_s7_sensitive_primary + - analyse_dataset_infants_rsv_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_rsv_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_rsv_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_rsv_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_rsv_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_rsv_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_rsv_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_rsv_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_rsv_full_s1_sensitive_primary + - analyse_dataset_infants_rsv_full_s2_sensitive_primary + - analyse_dataset_infants_rsv_full_s3_sensitive_primary + - analyse_dataset_infants_rsv_full_s4_sensitive_primary + - analyse_dataset_infants_rsv_full_s5_sensitive_primary + - analyse_dataset_infants_rsv_full_s6_sensitive_primary + - analyse_dataset_infants_rsv_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2016_2017.csv + csv: output/results/collated/infants_rsv_sensitivity_model_outputs_collated.csv - describe_cohort_infants_s1: - run: r:latest analysis/cohort_description.R infants season1_start_date season1_end_date sensitive secondary - needs: [process_dataset_infants_s1_sens_sec] + collate_flu_sensitivity_model_outputs_tables_infants: + run: r:latest analysis/flu_sensitivity_model_outputs_table_collation.R infants + infants + needs: + - analyse_dataset_infants_flu_ethnicity_s1_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_s2_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_s3_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_s4_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_s5_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_s6_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_s7_sensitive_primary + - analyse_dataset_infants_flu_ses_s1_sensitive_primary + - analyse_dataset_infants_flu_ses_s2_sensitive_primary + - analyse_dataset_infants_flu_ses_s3_sensitive_primary + - analyse_dataset_infants_flu_ses_s4_sensitive_primary + - analyse_dataset_infants_flu_ses_s5_sensitive_primary + - analyse_dataset_infants_flu_ses_s6_sensitive_primary + - analyse_dataset_infants_flu_ses_s7_sensitive_primary + - analyse_dataset_infants_flu_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_flu_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_flu_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_flu_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_flu_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_flu_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_flu_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_flu_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_flu_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_flu_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_flu_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_flu_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_flu_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_flu_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_flu_full_s1_sensitive_primary + - analyse_dataset_infants_flu_full_s2_sensitive_primary + - analyse_dataset_infants_flu_full_s3_sensitive_primary + - analyse_dataset_infants_flu_full_s4_sensitive_primary + - analyse_dataset_infants_flu_full_s5_sensitive_primary + - analyse_dataset_infants_flu_full_s6_sensitive_primary + - analyse_dataset_infants_flu_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2016_2017.csv + csv: output/results/collated/infants_flu_sensitivity_model_outputs_collated.csv -## season 7 (2022/23) - cohort description + collate_covid_sensitivity_model_outputs_tables_infants: + run: r:latest analysis/covid_sensitivity_model_outputs_table_collation.R infants + infants + needs: + - analyse_dataset_infants_covid_ethnicity_s4_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_s5_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_s6_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_s7_sensitive_primary + - analyse_dataset_infants_covid_ses_s4_sensitive_primary + - analyse_dataset_infants_covid_ses_s5_sensitive_primary + - analyse_dataset_infants_covid_ses_s6_sensitive_primary + - analyse_dataset_infants_covid_ses_s7_sensitive_primary + - analyse_dataset_infants_covid_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_covid_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_covid_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_covid_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_covid_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_covid_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_covid_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_covid_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_covid_full_s4_sensitive_primary + - analyse_dataset_infants_covid_full_s5_sensitive_primary + - analyse_dataset_infants_covid_full_s6_sensitive_primary + - analyse_dataset_infants_covid_full_s7_sensitive_primary + outputs: + moderately_sensitive: + csv: output/results/collated/infants_covid_sensitivity_model_outputs_collated.csv - describe_cohort_adults_s7: - run: r:latest analysis/cohort_description.R adults season7_start_date season7_end_date sensitive secondary - needs: [process_dataset_adults_s7_sens_sec] + collate_overall_and_all_cause_sensitivity_model_outputs_tables_infants: + run: r:latest analysis/overall_and_all_cause_sensitivity_model_outputs_table_collation.R + infants infants + needs: + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s2_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s6_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s7_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s1_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s2_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s4_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s5_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s6_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_s7_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_full_s1_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_full_s2_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_full_s3_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_full_s4_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_full_s5_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_full_s6_sensitive_primary + - analyse_dataset_infants_overall_and_all_cause_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2022_2023.csv + csv: output/results/collated/infants_overall_and_all_cause_sensitivity_model_outputs_collated.csv + + ## # # # # # # # # # # # # # # # # # # # + ## End + ## # # # # # # # # # # # # # # # # # # # +