diff --git a/actions.txt b/actions.txt index 1482413..84423bf 100644 --- a/actions.txt +++ b/actions.txt @@ -19,5 +19,5 @@ describe_cohort_older_adults_s1 describe_cohort_older_adults_s2 describe_cohort_ 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 +collate_flow_chart_tables_older_adults collate_table1_tables_older_adults collate_rates_tables_specific_primary_older_adults collate_rates_tables_sensitive_primary_older_adults collate_rates_tables_sensitive_secondary_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_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_sensitive_secondary_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_specific_primary_children_and_adolescents collate_rates_tables_sensitive_primary_children_and_adolescents collate_rates_tables_sensitive_secondary_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_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_sensitive_secondary_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 index 58a30a4..6f63279 100644 --- a/create-project.R +++ b/create-project.R @@ -768,7 +768,7 @@ action_finalise <- function(cohort) { action( name = glue("collate_flow_chart_tables_{cohort}"), - run = glue("r:latest analysis/flow_chart_table_collation.R {cohort}"), + run = glue("r:latest analysis/collation_code/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"), @@ -778,12 +778,27 @@ action_finalise <- function(cohort) { 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"), + csv = glue("output/collated/descriptive/{cohort}_flow_chart_collated.csv"), ) ), action( name = glue("collate_table1_tables_{cohort}"), - run = glue("r:latest analysis/table1_table_collation.R {cohort}"), + run = glue("r:latest analysis/collation_code/table1_table_collation.R {cohort}"), + arguments = c(cohort), + needs = list(glue("describe_cohort_{cohort}_s1"), + glue("describe_cohort_{cohort}_s2"), + glue("describe_cohort_{cohort}_s3"), + glue("describe_cohort_{cohort}_s4"), + glue("describe_cohort_{cohort}_s5"), + glue("describe_cohort_{cohort}_s6"), + glue("describe_cohort_{cohort}_s7")), + moderately_sensitive = lst( + csv = glue("output/collated/descriptive/{cohort}_table1_collated.csv")) + ), + + action( + name = glue("collate_rates_tables_specific_primary_{cohort}"), + run = glue("r:latest analysis/collation_code/rates_table_specific_primary_collation.R {cohort}"), arguments = c(cohort), needs = list(glue("describe_dataset_{cohort}_s1_specific_primary"), glue("describe_dataset_{cohort}_s2_specific_primary"), @@ -791,8 +806,16 @@ action_finalise <- function(cohort) { 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}_s7_specific_primary")), + moderately_sensitive = lst( + csv = glue("output/collated/descriptive/{cohort}_rates_specific_primary_collated.csv")) + ), + + action( + name = glue("collate_rates_tables_sensitive_primary_{cohort}"), + run = glue("r:latest analysis/collation_code/rates_table_sensitive_primary_collation.R {cohort}"), + arguments = c(cohort), + needs = list(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"), @@ -800,34 +823,27 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/descriptive/{cohort}_rates_sensitive_primary_collated.csv")) ), action( - name = glue("collate_rates_tables_{cohort}"), - run = glue("r:latest analysis/rates_table_collation.R {cohort}"), + name = glue("collate_rates_tables_sensitive_secondary_{cohort}"), + run = glue("r:latest analysis/collation_code/rates_table_sensitive_secondary_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")), + needs = list(glue("describe_dataset_{cohort}_s1_sensitive_secondary"), + glue("describe_dataset_{cohort}_s2_sensitive_secondary"), + glue("describe_dataset_{cohort}_s3_sensitive_secondary"), + glue("describe_dataset_{cohort}_s4_sensitive_secondary"), + glue("describe_dataset_{cohort}_s5_sensitive_secondary"), + glue("describe_dataset_{cohort}_s6_sensitive_secondary"), + glue("describe_dataset_{cohort}_s7_sensitive_secondary")), moderately_sensitive = lst( - csv = glue("output/results/collated/{cohort}_rates_collated.csv")) + csv = glue("output/collated/descriptive/{cohort}_rates_sensitive_secondary_collated.csv")) ), action( name = glue("collate_rsv_model_outputs_tables_{cohort}"), - run = glue("r:latest analysis/rsv_model_outputs_table_collation.R {cohort}"), + run = glue("r:latest analysis/collation_code/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"), @@ -879,12 +895,12 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/analytic/{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}"), + run = glue("r:latest analysis/collation_code/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"), @@ -936,12 +952,12 @@ action_finalise <- function(cohort) { 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")) + glue("output/collated/analytic/{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}"), + run = glue("r:latest analysis/collation_code/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"), @@ -972,12 +988,12 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/analytic/{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}"), + run = glue("r:latest analysis/collation_code/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"), @@ -1029,12 +1045,12 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/analytic/{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}"), + run = glue("r:latest analysis/collation_code/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"), @@ -1086,12 +1102,12 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/analytic/{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}"), + run = glue("r:latest analysis/collation_code/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"), @@ -1143,12 +1159,12 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/analytic/{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}"), + run = glue("r:latest analysis/collation_code/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"), @@ -1179,12 +1195,12 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/analytic/{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}"), + run = glue("r:latest analysis/collation_code/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"), @@ -1236,7 +1252,7 @@ action_finalise <- function(cohort) { 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")) + csv = glue("output/collated/analytic/{cohort}_overall_and_all_cause_sensitivity_model_outputs_collated.csv")) ) ) } @@ -1596,4 +1612,19 @@ names(actions_list) %>% tibble(action=.) %>% stop("Backend not recognised") } +##filter actions based on prefix +actions_list %>% + names() %>% + str_subset("^collate_rates") %>% + 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("filtered_actions.txt")) diff --git a/filtered_actions.txt b/filtered_actions.txt new file mode 100644 index 0000000..5951808 --- /dev/null +++ b/filtered_actions.txt @@ -0,0 +1 @@ +collate_rates_tables_specific_primary_older_adults collate_rates_tables_sensitive_primary_older_adults collate_rates_tables_sensitive_secondary_older_adults collate_rates_tables_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_sensitive_secondary_adults collate_rates_tables_specific_primary_children_and_adolescents collate_rates_tables_sensitive_primary_children_and_adolescents collate_rates_tables_sensitive_secondary_children_and_adolescents collate_rates_tables_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_sensitive_secondary_infants diff --git a/project.yaml b/project.yaml index 9b36af8..cf25ddb 100644 --- a/project.yaml +++ b/project.yaml @@ -43471,7 +43471,8 @@ actions: ## # # # # # # # # # # # # # # # # # # # collate_flow_chart_tables_older_adults: - run: r:latest analysis/flow_chart_table_collation.R older_adults older_adults + run: r:latest analysis/collation_code/flow_chart_table_collation.R older_adults + older_adults needs: - process_flow_chart_data_older_adults_s1 - process_flow_chart_data_older_adults_s2 @@ -43482,10 +43483,25 @@ actions: - process_flow_chart_data_older_adults_s7 outputs: moderately_sensitive: - csv: output/results/collated/older_adults_flow_chart_collated.csv + csv: output/collated/descriptive/older_adults_flow_chart_collated.csv collate_table1_tables_older_adults: - run: r:latest analysis/table1_table_collation.R older_adults older_adults + run: r:latest analysis/collation_code/table1_table_collation.R older_adults older_adults + needs: + - 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 + outputs: + moderately_sensitive: + csv: output/collated/descriptive/older_adults_table1_collated.csv + + collate_rates_tables_specific_primary_older_adults: + run: r:latest analysis/collation_code/rates_table_specific_primary_collation.R + older_adults older_adults needs: - describe_dataset_older_adults_s1_specific_primary - describe_dataset_older_adults_s2_specific_primary @@ -43494,6 +43510,14 @@ actions: - describe_dataset_older_adults_s5_specific_primary - describe_dataset_older_adults_s6_specific_primary - describe_dataset_older_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/collated/descriptive/older_adults_rates_specific_primary_collated.csv + + collate_rates_tables_sensitive_primary_older_adults: + run: r:latest analysis/collation_code/rates_table_sensitive_primary_collation.R + older_adults older_adults + needs: - describe_dataset_older_adults_s1_sensitive_primary - describe_dataset_older_adults_s2_sensitive_primary - describe_dataset_older_adults_s3_sensitive_primary @@ -43503,31 +43527,26 @@ actions: - describe_dataset_older_adults_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_table1_collated.csv + csv: output/collated/descriptive/older_adults_rates_sensitive_primary_collated.csv - collate_rates_tables_older_adults: - run: r:latest analysis/rates_table_collation.R older_adults older_adults + collate_rates_tables_sensitive_secondary_older_adults: + run: r:latest analysis/collation_code/rates_table_sensitive_secondary_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 + - describe_dataset_older_adults_s1_sensitive_secondary + - describe_dataset_older_adults_s2_sensitive_secondary + - describe_dataset_older_adults_s3_sensitive_secondary + - describe_dataset_older_adults_s4_sensitive_secondary + - describe_dataset_older_adults_s5_sensitive_secondary + - describe_dataset_older_adults_s6_sensitive_secondary + - describe_dataset_older_adults_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_rates_collated.csv + csv: output/collated/descriptive/older_adults_rates_sensitive_secondary_collated.csv collate_rsv_model_outputs_tables_older_adults: - run: r:latest analysis/rsv_model_outputs_table_collation.R older_adults older_adults + run: r:latest analysis/collation_code/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 @@ -43580,10 +43599,11 @@ actions: - analyse_dataset_older_adults_rsv_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_rsv_model_outputs_collated.csv + csv: output/collated/analytic/older_adults_rsv_model_outputs_collated.csv collate_flu_model_outputs_tables_older_adults: - run: r:latest analysis/flu_model_outputs_table_collation.R older_adults older_adults + run: r:latest analysis/collation_code/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 @@ -43636,10 +43656,11 @@ actions: - analyse_dataset_older_adults_flu_full_s7_specific_primary outputs: moderately_sensitive: - glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv"): output/results/collated/older_adults_flu_model_outputs_collated.csv + glue("output/collated/analytic/{cohort}_flu_model_outputs_collated.csv"): output/collated/analytic/older_adults_flu_model_outputs_collated.csv collate_covid_model_outputs_tables_older_adults: - run: r:latest analysis/covid_model_outputs_table_collation.R older_adults older_adults + run: r:latest analysis/collation_code/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 @@ -43671,11 +43692,11 @@ actions: - analyse_dataset_older_adults_covid_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_covid_model_outputs_collated.csv + csv: output/collated/analytic/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 + run: r:latest analysis/collation_code/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 @@ -43728,11 +43749,11 @@ actions: - analyse_dataset_older_adults_overall_and_all_cause_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_overall_and_all_cause_model_outputs_collated.csv + csv: output/collated/analytic/older_adults_overall_and_all_cause_model_outputs_collated.csv collate_rsv_sensitivity_model_outputs_tables_older_adults: - run: r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R older_adults - older_adults + run: r:latest analysis/collation_code/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 @@ -43785,11 +43806,11 @@ actions: - analyse_dataset_older_adults_rsv_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_rsv_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/older_adults_rsv_sensitivity_model_outputs_collated.csv collate_flu_sensitivity_model_outputs_tables_older_adults: - run: r:latest analysis/flu_sensitivity_model_outputs_table_collation.R older_adults - older_adults + run: r:latest analysis/collation_code/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 @@ -43842,11 +43863,11 @@ actions: - analyse_dataset_older_adults_flu_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_flu_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/older_adults_flu_sensitivity_model_outputs_collated.csv collate_covid_sensitivity_model_outputs_tables_older_adults: - run: r:latest analysis/covid_sensitivity_model_outputs_table_collation.R older_adults - older_adults + run: r:latest analysis/collation_code/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 @@ -43878,10 +43899,10 @@ actions: - analyse_dataset_older_adults_covid_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_covid_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/older_adults_covid_sensitivity_model_outputs_collated.csv 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 + run: r:latest analysis/collation_code/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 @@ -43935,10 +43956,10 @@ actions: - analyse_dataset_older_adults_overall_and_all_cause_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/older_adults_overall_and_all_cause_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/older_adults_overall_and_all_cause_sensitivity_model_outputs_collated.csv collate_flow_chart_tables_adults: - run: r:latest analysis/flow_chart_table_collation.R adults adults + run: r:latest analysis/collation_code/flow_chart_table_collation.R adults adults needs: - process_flow_chart_data_adults_s1 - process_flow_chart_data_adults_s2 @@ -43949,10 +43970,25 @@ actions: - process_flow_chart_data_adults_s7 outputs: moderately_sensitive: - csv: output/results/collated/adults_flow_chart_collated.csv + csv: output/collated/descriptive/adults_flow_chart_collated.csv collate_table1_tables_adults: - run: r:latest analysis/table1_table_collation.R adults adults + run: r:latest analysis/collation_code/table1_table_collation.R adults adults + needs: + - 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 + outputs: + moderately_sensitive: + csv: output/collated/descriptive/adults_table1_collated.csv + + collate_rates_tables_specific_primary_adults: + run: r:latest analysis/collation_code/rates_table_specific_primary_collation.R + adults adults needs: - describe_dataset_adults_s1_specific_primary - describe_dataset_adults_s2_specific_primary @@ -43961,6 +43997,14 @@ actions: - describe_dataset_adults_s5_specific_primary - describe_dataset_adults_s6_specific_primary - describe_dataset_adults_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/collated/descriptive/adults_rates_specific_primary_collated.csv + + collate_rates_tables_sensitive_primary_adults: + run: r:latest analysis/collation_code/rates_table_sensitive_primary_collation.R + adults adults + needs: - describe_dataset_adults_s1_sensitive_primary - describe_dataset_adults_s2_sensitive_primary - describe_dataset_adults_s3_sensitive_primary @@ -43970,31 +44014,26 @@ actions: - describe_dataset_adults_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_table1_collated.csv + csv: output/collated/descriptive/adults_rates_sensitive_primary_collated.csv - collate_rates_tables_adults: - run: r:latest analysis/rates_table_collation.R adults adults + collate_rates_tables_sensitive_secondary_adults: + run: r:latest analysis/collation_code/rates_table_sensitive_secondary_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 + - describe_dataset_adults_s1_sensitive_secondary + - describe_dataset_adults_s2_sensitive_secondary + - describe_dataset_adults_s3_sensitive_secondary + - describe_dataset_adults_s4_sensitive_secondary + - describe_dataset_adults_s5_sensitive_secondary + - describe_dataset_adults_s6_sensitive_secondary + - describe_dataset_adults_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/collated/adults_rates_collated.csv + csv: output/collated/descriptive/adults_rates_sensitive_secondary_collated.csv collate_rsv_model_outputs_tables_adults: - run: r:latest analysis/rsv_model_outputs_table_collation.R adults adults + run: r:latest analysis/collation_code/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 @@ -44047,10 +44086,11 @@ actions: - analyse_dataset_adults_rsv_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_rsv_model_outputs_collated.csv + csv: output/collated/analytic/adults_rsv_model_outputs_collated.csv collate_flu_model_outputs_tables_adults: - run: r:latest analysis/flu_model_outputs_table_collation.R adults adults + run: r:latest analysis/collation_code/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 @@ -44103,10 +44143,11 @@ actions: - analyse_dataset_adults_flu_full_s7_specific_primary outputs: moderately_sensitive: - glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv"): output/results/collated/adults_flu_model_outputs_collated.csv + glue("output/collated/analytic/{cohort}_flu_model_outputs_collated.csv"): output/collated/analytic/adults_flu_model_outputs_collated.csv collate_covid_model_outputs_tables_adults: - run: r:latest analysis/covid_model_outputs_table_collation.R adults adults + run: r:latest analysis/collation_code/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 @@ -44138,11 +44179,11 @@ actions: - analyse_dataset_adults_covid_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_covid_model_outputs_collated.csv + csv: output/collated/analytic/adults_covid_model_outputs_collated.csv collate_overall_and_all_cause_model_outputs_tables_adults: - run: r:latest analysis/overall_and_all_cause_model_outputs_table_collation.R adults - adults + run: r:latest analysis/collation_code/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 @@ -44195,11 +44236,11 @@ actions: - analyse_dataset_adults_overall_and_all_cause_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_overall_and_all_cause_model_outputs_collated.csv + csv: output/collated/analytic/adults_overall_and_all_cause_model_outputs_collated.csv collate_rsv_sensitivity_model_outputs_tables_adults: - run: r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R adults - adults + run: r:latest analysis/collation_code/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 @@ -44252,11 +44293,11 @@ actions: - analyse_dataset_adults_rsv_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_rsv_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/adults_rsv_sensitivity_model_outputs_collated.csv collate_flu_sensitivity_model_outputs_tables_adults: - run: r:latest analysis/flu_sensitivity_model_outputs_table_collation.R adults - adults + run: r:latest analysis/collation_code/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 @@ -44309,11 +44350,11 @@ actions: - analyse_dataset_adults_flu_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_flu_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/adults_flu_sensitivity_model_outputs_collated.csv collate_covid_sensitivity_model_outputs_tables_adults: - run: r:latest analysis/covid_sensitivity_model_outputs_table_collation.R adults - adults + run: r:latest analysis/collation_code/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 @@ -44345,10 +44386,10 @@ actions: - analyse_dataset_adults_covid_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_covid_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/adults_covid_sensitivity_model_outputs_collated.csv collate_overall_and_all_cause_sensitivity_model_outputs_tables_adults: - run: r:latest analysis/overall_and_all_cause_sensitivity_model_outputs_table_collation.R + run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R adults adults needs: - analyse_dataset_adults_overall_and_all_cause_ethnicity_s1_sensitive_primary @@ -44402,10 +44443,11 @@ actions: - analyse_dataset_adults_overall_and_all_cause_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/adults_overall_and_all_cause_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/adults_overall_and_all_cause_sensitivity_model_outputs_collated.csv collate_flow_chart_tables_children_and_adolescents: - run: r:latest analysis/flow_chart_table_collation.R children_and_adolescents children_and_adolescents + run: r:latest analysis/collation_code/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 @@ -44416,10 +44458,26 @@ actions: - process_flow_chart_data_children_and_adolescents_s7 outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_flow_chart_collated.csv + csv: output/collated/descriptive/children_and_adolescents_flow_chart_collated.csv collate_table1_tables_children_and_adolescents: - run: r:latest analysis/table1_table_collation.R children_and_adolescents children_and_adolescents + run: r:latest analysis/collation_code/table1_table_collation.R children_and_adolescents + children_and_adolescents + needs: + - 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 + outputs: + moderately_sensitive: + csv: output/collated/descriptive/children_and_adolescents_table1_collated.csv + + collate_rates_tables_specific_primary_children_and_adolescents: + run: r:latest analysis/collation_code/rates_table_specific_primary_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 @@ -44428,6 +44486,14 @@ actions: - describe_dataset_children_and_adolescents_s5_specific_primary - describe_dataset_children_and_adolescents_s6_specific_primary - describe_dataset_children_and_adolescents_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/collated/descriptive/children_and_adolescents_rates_specific_primary_collated.csv + + collate_rates_tables_sensitive_primary_children_and_adolescents: + run: r:latest analysis/collation_code/rates_table_sensitive_primary_collation.R + children_and_adolescents children_and_adolescents + needs: - describe_dataset_children_and_adolescents_s1_sensitive_primary - describe_dataset_children_and_adolescents_s2_sensitive_primary - describe_dataset_children_and_adolescents_s3_sensitive_primary @@ -44437,31 +44503,25 @@ actions: - describe_dataset_children_and_adolescents_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_table1_collated.csv + csv: output/collated/descriptive/children_and_adolescents_rates_sensitive_primary_collated.csv - collate_rates_tables_children_and_adolescents: - run: r:latest analysis/rates_table_collation.R children_and_adolescents children_and_adolescents + collate_rates_tables_sensitive_secondary_children_and_adolescents: + run: r:latest analysis/collation_code/rates_table_sensitive_secondary_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 + - describe_dataset_children_and_adolescents_s1_sensitive_secondary + - describe_dataset_children_and_adolescents_s2_sensitive_secondary + - describe_dataset_children_and_adolescents_s3_sensitive_secondary + - describe_dataset_children_and_adolescents_s4_sensitive_secondary + - describe_dataset_children_and_adolescents_s5_sensitive_secondary + - describe_dataset_children_and_adolescents_s6_sensitive_secondary + - describe_dataset_children_and_adolescents_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_rates_collated.csv + csv: output/collated/descriptive/children_and_adolescents_rates_sensitive_secondary_collated.csv collate_rsv_model_outputs_tables_children_and_adolescents: - run: r:latest analysis/rsv_model_outputs_table_collation.R children_and_adolescents + run: r:latest analysis/collation_code/rsv_model_outputs_table_collation.R children_and_adolescents children_and_adolescents needs: - analyse_dataset_children_and_adolescents_rsv_ethnicity_s1_specific_primary @@ -44515,10 +44575,10 @@ actions: - 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 + csv: output/collated/analytic/children_and_adolescents_rsv_model_outputs_collated.csv collate_flu_model_outputs_tables_children_and_adolescents: - run: r:latest analysis/flu_model_outputs_table_collation.R children_and_adolescents + run: r:latest analysis/collation_code/flu_model_outputs_table_collation.R children_and_adolescents children_and_adolescents needs: - analyse_dataset_children_and_adolescents_flu_ethnicity_s1_specific_primary @@ -44572,10 +44632,10 @@ actions: - analyse_dataset_children_and_adolescents_flu_full_s7_specific_primary outputs: moderately_sensitive: - glue("output/results/collated/{cohort}_flu_model_outputs_collated.csv"): output/results/collated/children_and_adolescents_flu_model_outputs_collated.csv + glue("output/collated/analytic/{cohort}_flu_model_outputs_collated.csv"): output/collated/analytic/children_and_adolescents_flu_model_outputs_collated.csv collate_covid_model_outputs_tables_children_and_adolescents: - run: r:latest analysis/covid_model_outputs_table_collation.R children_and_adolescents + run: r:latest analysis/collation_code/covid_model_outputs_table_collation.R children_and_adolescents children_and_adolescents needs: - analyse_dataset_children_and_adolescents_covid_ethnicity_s4_specific_primary @@ -44608,11 +44668,11 @@ actions: - analyse_dataset_children_and_adolescents_covid_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_covid_model_outputs_collated.csv + csv: output/collated/analytic/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 + run: r:latest analysis/collation_code/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 @@ -44665,11 +44725,11 @@ actions: - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_overall_and_all_cause_model_outputs_collated.csv + csv: output/collated/analytic/children_and_adolescents_overall_and_all_cause_model_outputs_collated.csv 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 + run: r:latest analysis/collation_code/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 @@ -44722,11 +44782,11 @@ actions: - analyse_dataset_children_and_adolescents_rsv_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_rsv_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/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 + run: r:latest analysis/collation_code/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 @@ -44779,11 +44839,11 @@ actions: - analyse_dataset_children_and_adolescents_flu_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_flu_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/children_and_adolescents_flu_sensitivity_model_outputs_collated.csv 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 + run: r:latest analysis/collation_code/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 @@ -44815,10 +44875,10 @@ actions: - analyse_dataset_children_and_adolescents_covid_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_covid_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/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 + run: r:latest analysis/collation_code/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 @@ -44872,10 +44932,10 @@ actions: - analyse_dataset_children_and_adolescents_overall_and_all_cause_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/children_and_adolescents_overall_and_all_cause_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/children_and_adolescents_overall_and_all_cause_sensitivity_model_outputs_collated.csv collate_flow_chart_tables_infants: - run: r:latest analysis/flow_chart_table_collation.R infants infants + run: r:latest analysis/collation_code/flow_chart_table_collation.R infants infants needs: - process_flow_chart_data_infants_s1 - process_flow_chart_data_infants_s2 @@ -44886,10 +44946,25 @@ actions: - process_flow_chart_data_infants_s7 outputs: moderately_sensitive: - csv: output/results/collated/infants_flow_chart_collated.csv + csv: output/collated/descriptive/infants_flow_chart_collated.csv collate_table1_tables_infants: - run: r:latest analysis/table1_table_collation.R infants infants + run: r:latest analysis/collation_code/table1_table_collation.R infants infants + needs: + - 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 + outputs: + moderately_sensitive: + csv: output/collated/descriptive/infants_table1_collated.csv + + collate_rates_tables_specific_primary_infants: + run: r:latest analysis/collation_code/rates_table_specific_primary_collation.R + infants infants needs: - describe_dataset_infants_s1_specific_primary - describe_dataset_infants_s2_specific_primary @@ -44898,6 +44973,14 @@ actions: - describe_dataset_infants_s5_specific_primary - describe_dataset_infants_s6_specific_primary - describe_dataset_infants_s7_specific_primary + outputs: + moderately_sensitive: + csv: output/collated/descriptive/infants_rates_specific_primary_collated.csv + + collate_rates_tables_sensitive_primary_infants: + run: r:latest analysis/collation_code/rates_table_sensitive_primary_collation.R + infants infants + needs: - describe_dataset_infants_s1_sensitive_primary - describe_dataset_infants_s2_sensitive_primary - describe_dataset_infants_s3_sensitive_primary @@ -44907,31 +44990,26 @@ actions: - describe_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_table1_collated.csv + csv: output/collated/descriptive/infants_rates_sensitive_primary_collated.csv - collate_rates_tables_infants: - run: r:latest analysis/rates_table_collation.R infants infants + collate_rates_tables_sensitive_secondary_infants: + run: r:latest analysis/collation_code/rates_table_sensitive_secondary_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 + - describe_dataset_infants_s1_sensitive_secondary + - describe_dataset_infants_s2_sensitive_secondary + - describe_dataset_infants_s3_sensitive_secondary + - describe_dataset_infants_s4_sensitive_secondary + - describe_dataset_infants_s5_sensitive_secondary + - describe_dataset_infants_s6_sensitive_secondary + - describe_dataset_infants_s7_sensitive_secondary outputs: moderately_sensitive: - csv: output/results/collated/infants_rates_collated.csv + csv: output/collated/descriptive/infants_rates_sensitive_secondary_collated.csv collate_rsv_model_outputs_tables_infants: - run: r:latest analysis/rsv_model_outputs_table_collation.R infants infants + run: r:latest analysis/collation_code/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 @@ -44984,10 +45062,11 @@ actions: - analyse_dataset_infants_rsv_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_rsv_model_outputs_collated.csv + csv: output/collated/analytic/infants_rsv_model_outputs_collated.csv collate_flu_model_outputs_tables_infants: - run: r:latest analysis/flu_model_outputs_table_collation.R infants infants + run: r:latest analysis/collation_code/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 @@ -45040,10 +45119,11 @@ actions: - 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 + glue("output/collated/analytic/{cohort}_flu_model_outputs_collated.csv"): output/collated/analytic/infants_flu_model_outputs_collated.csv collate_covid_model_outputs_tables_infants: - run: r:latest analysis/covid_model_outputs_table_collation.R infants infants + run: r:latest analysis/collation_code/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 @@ -45075,11 +45155,11 @@ actions: - analyse_dataset_infants_covid_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_covid_model_outputs_collated.csv + csv: output/collated/analytic/infants_covid_model_outputs_collated.csv collate_overall_and_all_cause_model_outputs_tables_infants: - run: r:latest analysis/overall_and_all_cause_model_outputs_table_collation.R infants - infants + run: r:latest analysis/collation_code/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 @@ -45132,11 +45212,11 @@ actions: - analyse_dataset_infants_overall_and_all_cause_full_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_overall_and_all_cause_model_outputs_collated.csv + csv: output/collated/analytic/infants_overall_and_all_cause_model_outputs_collated.csv collate_rsv_sensitivity_model_outputs_tables_infants: - run: r:latest analysis/rsv_sensitivity_model_outputs_table_collation.R infants - infants + run: r:latest analysis/collation_code/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 @@ -45189,11 +45269,11 @@ actions: - analyse_dataset_infants_rsv_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_rsv_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/infants_rsv_sensitivity_model_outputs_collated.csv collate_flu_sensitivity_model_outputs_tables_infants: - run: r:latest analysis/flu_sensitivity_model_outputs_table_collation.R infants - infants + run: r:latest analysis/collation_code/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 @@ -45246,11 +45326,11 @@ actions: - analyse_dataset_infants_flu_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_flu_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/infants_flu_sensitivity_model_outputs_collated.csv collate_covid_sensitivity_model_outputs_tables_infants: - run: r:latest analysis/covid_sensitivity_model_outputs_table_collation.R infants - infants + run: r:latest analysis/collation_code/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 @@ -45282,10 +45362,10 @@ actions: - analyse_dataset_infants_covid_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_covid_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/infants_covid_sensitivity_model_outputs_collated.csv collate_overall_and_all_cause_sensitivity_model_outputs_tables_infants: - run: r:latest analysis/overall_and_all_cause_sensitivity_model_outputs_table_collation.R + run: r:latest analysis/collation_code/overall_and_all_cause_sensitivity_model_outputs_table_collation.R infants infants needs: - analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_sensitive_primary @@ -45339,7 +45419,7 @@ actions: - analyse_dataset_infants_overall_and_all_cause_full_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/collated/infants_overall_and_all_cause_sensitivity_model_outputs_collated.csv + csv: output/collated/analytic/infants_overall_and_all_cause_sensitivity_model_outputs_collated.csv ## # # # # # # # # # # # # # # # # # # # ## End