From 463b92a53c124eca16ce0bc184dc31f1260889a5 Mon Sep 17 00:00:00 2001 From: Em Prestige Date: Wed, 25 Sep 2024 12:18:14 +0100 Subject: [PATCH] update yaml --- actions.txt | 18 +- create-project.R | 1478 ++++++++++++++++-- project.yaml | 3796 +++++++++++++++++++--------------------------- 3 files changed, 2930 insertions(+), 2362 deletions(-) diff --git a/actions.txt b/actions.txt index d8dfd46..c103e52 100644 --- a/actions.txt +++ b/actions.txt @@ -11,14 +11,14 @@ generate_dataset_older_adults_s1_sensitive_primary process_dataset_older_adults_ generate_dataset_adults_s1_sensitive_primary process_dataset_adults_s1_sensitive_primary describe_dataset_adults_s1_sensitive_primary analyse_dataset_adults_rsv_s1_sensitive_primary analyse_dataset_adults_rsv_further_s1_sensitive_primary analyse_dataset_adults_flu_s1_sensitive_primary analyse_dataset_adults_flu_further_s1_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s1_sensitive_primary analyse_dataset_adults_overall_and_all_cause_further_s1_sensitive_primary generate_dataset_adults_s2_sensitive_primary process_dataset_adults_s2_sensitive_primary describe_dataset_adults_s2_sensitive_primary analyse_dataset_adults_rsv_s2_sensitive_primary analyse_dataset_adults_rsv_further_s2_sensitive_primary analyse_dataset_adults_flu_s2_sensitive_primary analyse_dataset_adults_flu_further_s2_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s2_sensitive_primary analyse_dataset_adults_overall_and_all_cause_further_s2_sensitive_primary generate_dataset_adults_s3_sensitive_primary process_dataset_adults_s3_sensitive_primary describe_dataset_adults_s3_sensitive_primary analyse_dataset_adults_rsv_s3_sensitive_primary analyse_dataset_adults_rsv_further_s3_sensitive_primary analyse_dataset_adults_flu_s3_sensitive_primary analyse_dataset_adults_flu_further_s3_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s3_sensitive_primary 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analyse_dataset_infants_flu_s2_specific_secondary analyse_dataset_infants_flu_further_s2_specific_secondary analyse_dataset_infants_overall_and_all_cause_s2_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s2_specific_secondary generate_dataset_infants_s3_specific_secondary process_dataset_infants_s3_specific_secondary describe_dataset_infants_s3_specific_secondary analyse_dataset_infants_rsv_s3_specific_secondary analyse_dataset_infants_rsv_further_s3_specific_secondary analyse_dataset_infants_flu_s3_specific_secondary analyse_dataset_infants_flu_further_s3_specific_secondary analyse_dataset_infants_overall_and_all_cause_s3_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s3_specific_secondary generate_dataset_infants_s4_specific_secondary process_dataset_infants_s4_specific_secondary describe_dataset_infants_s4_specific_secondary analyse_dataset_infants_rsv_s4_specific_secondary analyse_dataset_infants_rsv_further_s4_specific_secondary analyse_dataset_infants_flu_s4_specific_secondary analyse_dataset_infants_flu_further_s4_specific_secondary analyse_dataset_infants_overall_and_all_cause_s4_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s4_specific_secondary analyse_dataset_infants_covid_s4_specific_secondary analyse_dataset_infants_covid_further_s4_specific_secondary generate_dataset_infants_s5_specific_secondary process_dataset_infants_s5_specific_secondary describe_dataset_infants_s5_specific_secondary analyse_dataset_infants_rsv_s5_specific_secondary analyse_dataset_infants_rsv_further_s5_specific_secondary analyse_dataset_infants_flu_s5_specific_secondary analyse_dataset_infants_flu_further_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s5_specific_secondary analyse_dataset_infants_covid_s5_specific_secondary analyse_dataset_infants_covid_further_s5_specific_secondary generate_dataset_infants_s6_specific_secondary process_dataset_infants_s6_specific_secondary describe_dataset_infants_s6_specific_secondary analyse_dataset_infants_rsv_s6_specific_secondary analyse_dataset_infants_rsv_further_s6_specific_secondary analyse_dataset_infants_flu_s6_specific_secondary analyse_dataset_infants_flu_further_s6_specific_secondary analyse_dataset_infants_overall_and_all_cause_s6_specific_secondary analyse_dataset_infants_overall_and_all_cause_further_s6_specific_secondary analyse_dataset_infants_covid_s6_specific_secondary analyse_dataset_infants_covid_further_s6_specific_secondary generate_dataset_infants_s7_specific_secondary process_dataset_infants_s7_specific_secondary describe_dataset_infants_s7_specific_secondary analyse_dataset_infants_rsv_s7_specific_secondary analyse_dataset_infants_rsv_further_s7_specific_secondary analyse_dataset_infants_flu_s7_specific_secondary analyse_dataset_infants_flu_further_s7_specific_secondary 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describe_cohort_infants_s2 describe_cohort_infants_s3 describe_cohort_infants_s4 describe_cohort_infants_s5 describe_cohort_infants_s6 describe_cohort_infants_s7 +generate_dataset_older_adults_s1_specific_secondary process_cohort_older_adults_s1_specific_secondary describe_cohort_older_adults_s1 generate_dataset_older_adults_s2_specific_secondary process_cohort_older_adults_s2_specific_secondary describe_cohort_older_adults_s2 generate_dataset_older_adults_s3_specific_secondary process_cohort_older_adults_s3_specific_secondary describe_cohort_older_adults_s3 generate_dataset_older_adults_s4_specific_secondary process_cohort_older_adults_s4_specific_secondary describe_cohort_older_adults_s4 generate_dataset_older_adults_s5_specific_secondary process_cohort_older_adults_s5_specific_secondary describe_cohort_older_adults_s5 generate_dataset_older_adults_s6_specific_secondary process_cohort_older_adults_s6_specific_secondary describe_cohort_older_adults_s6 generate_dataset_older_adults_s7_specific_secondary process_cohort_older_adults_s7_specific_secondary describe_cohort_older_adults_s7 +generate_dataset_adults_s1_specific_secondary process_cohort_adults_s1_specific_secondary describe_cohort_adults_s1 generate_dataset_adults_s2_specific_secondary process_cohort_adults_s2_specific_secondary describe_cohort_adults_s2 generate_dataset_adults_s3_specific_secondary process_cohort_adults_s3_specific_secondary describe_cohort_adults_s3 generate_dataset_adults_s4_specific_secondary process_cohort_adults_s4_specific_secondary describe_cohort_adults_s4 generate_dataset_adults_s5_specific_secondary process_cohort_adults_s5_specific_secondary describe_cohort_adults_s5 generate_dataset_adults_s6_specific_secondary process_cohort_adults_s6_specific_secondary describe_cohort_adults_s6 generate_dataset_adults_s7_specific_secondary process_cohort_adults_s7_specific_secondary describe_cohort_adults_s7 +generate_dataset_children_and_adolescents_s1_specific_secondary process_cohort_children_and_adolescents_s1_specific_secondary describe_cohort_children_and_adolescents_s1 generate_dataset_children_and_adolescents_s2_specific_secondary process_cohort_children_and_adolescents_s2_specific_secondary describe_cohort_children_and_adolescents_s2 generate_dataset_children_and_adolescents_s3_specific_secondary process_cohort_children_and_adolescents_s3_specific_secondary describe_cohort_children_and_adolescents_s3 generate_dataset_children_and_adolescents_s4_specific_secondary process_cohort_children_and_adolescents_s4_specific_secondary describe_cohort_children_and_adolescents_s4 generate_dataset_children_and_adolescents_s5_specific_secondary process_cohort_children_and_adolescents_s5_specific_secondary describe_cohort_children_and_adolescents_s5 generate_dataset_children_and_adolescents_s6_specific_secondary process_cohort_children_and_adolescents_s6_specific_secondary describe_cohort_children_and_adolescents_s6 generate_dataset_children_and_adolescents_s7_specific_secondary process_cohort_children_and_adolescents_s7_specific_secondary describe_cohort_children_and_adolescents_s7 +generate_dataset_infants_s1_specific_secondary process_cohort_infants_s1_specific_secondary describe_cohort_infants_s1 generate_dataset_infants_s2_specific_secondary process_cohort_infants_s2_specific_secondary describe_cohort_infants_s2 generate_dataset_infants_s3_specific_secondary process_cohort_infants_s3_specific_secondary describe_cohort_infants_s3 generate_dataset_infants_s4_specific_secondary process_cohort_infants_s4_specific_secondary describe_cohort_infants_s4 generate_dataset_infants_s5_specific_secondary process_cohort_infants_s5_specific_secondary describe_cohort_infants_s5 generate_dataset_infants_s6_specific_secondary process_cohort_infants_s6_specific_secondary describe_cohort_infants_s6 generate_dataset_infants_s7_specific_secondary process_cohort_infants_s7_specific_secondary describe_cohort_infants_s7 +process_dataset_older_adults_s2_specific_secondary describe_dataset_older_adults_s2_specific_secondary analyse_dataset_older_adults_rsv_s2_specific_secondary analyse_dataset_older_adults_rsv_further_s2_specific_secondary analyse_dataset_older_adults_overall_and_all_cause_s2_specific_secondary analyse_dataset_older_adults_overall_and_all_cause_further_s2_specific_secondary process_dataset_older_adults_s3_specific_secondary describe_dataset_older_adults_s3_specific_secondary analyse_dataset_older_adults_flu_s3_specific_secondary analyse_dataset_older_adults_flu_further_s3_specific_secondary analyse_dataset_older_adults_overall_and_all_cause_s3_specific_secondary analyse_dataset_older_adults_overall_and_all_cause_further_s3_specific_secondary process_dataset_older_adults_s5_specific_secondary describe_dataset_older_adults_s5_specific_secondary analyse_dataset_older_adults_covid_s5_specific_secondary analyse_dataset_older_adults_covid_further_s5_specific_secondary analyse_dataset_older_adults_overall_and_all_cause_s5_specific_secondary analyse_dataset_older_adults_overall_and_all_cause_further_s5_specific_secondary +process_dataset_adults_s2_specific_secondary describe_dataset_adults_s2_specific_secondary analyse_dataset_adults_rsv_s2_specific_secondary analyse_dataset_adults_rsv_further_s2_specific_secondary analyse_dataset_adults_overall_and_all_cause_s2_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s2_specific_secondary process_dataset_adults_s3_specific_secondary describe_dataset_adults_s3_specific_secondary analyse_dataset_adults_flu_s3_specific_secondary analyse_dataset_adults_flu_further_s3_specific_secondary analyse_dataset_adults_overall_and_all_cause_s3_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s3_specific_secondary process_dataset_adults_s5_specific_secondary describe_dataset_adults_s5_specific_secondary analyse_dataset_adults_covid_s5_specific_secondary analyse_dataset_adults_covid_further_s5_specific_secondary analyse_dataset_adults_overall_and_all_cause_s5_specific_secondary analyse_dataset_adults_overall_and_all_cause_further_s5_specific_secondary +process_dataset_children_and_adolescents_s2_specific_secondary describe_dataset_children_and_adolescents_s2_specific_secondary analyse_dataset_children_and_adolescents_rsv_s2_specific_secondary analyse_dataset_children_and_adolescents_rsv_further_s2_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_s2_specific_secondary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_specific_secondary process_dataset_children_and_adolescents_s3_specific_secondary describe_dataset_children_and_adolescents_s3_specific_secondary analyse_dataset_children_and_adolescents_flu_s3_specific_secondary analyse_dataset_children_and_adolescents_flu_further_s3_specific_secondary 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analyse_dataset_infants_further_overall_and_all_cause_full_s3_specific_secondary process_dataset_infants_s5_specific_secondary describe_dataset_infants_s5_specific_secondary analyse_dataset_infants_covid_ethnicity_s5_specific_secondary analyse_dataset_infants_covid_ses_s5_specific_secondary analyse_dataset_infants_covid_hh_comp_s5_specific_secondary analyse_dataset_infants_covid_ethnicity_ses_s5_specific_secondary analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_secondary analyse_dataset_infants_covid_ses_hh_comp_s5_specific_secondary analyse_dataset_infants_covid_full_s5_specific_secondary analyse_dataset_infants_further_covid_ethnicity_s5_specific_secondary analyse_dataset_infantsfurther__covid_ses_s5_specific_secondary analyse_dataset_infants_further_covid_hh_comp_s5_specific_secondary analyse_dataset_infants_further_covid_ethnicity_ses_s5_specific_secondary analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_specific_secondary analyse_dataset_infants_further_covid_ses_hh_comp_s5_specific_secondary analyse_dataset_infants_further_covid_full_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_ses_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_specific_secondary analyse_dataset_infants_overall_and_all_cause_full_s5_specific_secondary analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_specific_secondary analyse_dataset_infantsfurther__overall_and_all_cause_ses_s5_specific_secondary analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_specific_secondary analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_specific_secondary analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_secondary analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_specific_secondary analyse_dataset_infants_further_overall_and_all_cause_full_s5_specific_secondary phenotype_sensitivity_older_adults_s1 phenotype_sensitivity_older_adults_s2 phenotype_sensitivity_older_adults_s3 phenotype_sensitivity_older_adults_s4 phenotype_sensitivity_older_adults_s5 phenotype_sensitivity_older_adults_s6 phenotype_sensitivity_older_adults_s7 phenotype_sensitivity_adults_s1 phenotype_sensitivity_adults_s2 phenotype_sensitivity_adults_s3 phenotype_sensitivity_adults_s4 phenotype_sensitivity_adults_s5 phenotype_sensitivity_adults_s6 phenotype_sensitivity_adults_s7 phenotype_sensitivity_children_and_adolescents_s1 phenotype_sensitivity_children_and_adolescents_s2 phenotype_sensitivity_children_and_adolescents_s3 phenotype_sensitivity_children_and_adolescents_s4 phenotype_sensitivity_children_and_adolescents_s5 phenotype_sensitivity_children_and_adolescents_s6 phenotype_sensitivity_children_and_adolescents_s7 @@ -31,5 +31,5 @@ process_dataset_older_adults_s1_sensitive_sensitivity describe_dataset_older_adu process_dataset_adults_s1_sensitive_sensitivity describe_dataset_adults_s1_sensitive_sensitivity analyse_dataset_adults_rsv_s1_sensitive_sensitivity analyse_dataset_adults_rsv_further_s1_sensitive_sensitivity analyse_dataset_adults_flu_s1_sensitive_sensitivity analyse_dataset_adults_flu_further_s1_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_s1_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_further_s1_sensitive_sensitivity process_dataset_adults_s2_sensitive_sensitivity describe_dataset_adults_s2_sensitive_sensitivity analyse_dataset_adults_rsv_s2_sensitive_sensitivity analyse_dataset_adults_rsv_further_s2_sensitive_sensitivity analyse_dataset_adults_flu_s2_sensitive_sensitivity analyse_dataset_adults_flu_further_s2_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_s2_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_further_s2_sensitive_sensitivity process_dataset_adults_s3_sensitive_sensitivity describe_dataset_adults_s3_sensitive_sensitivity analyse_dataset_adults_rsv_s3_sensitive_sensitivity analyse_dataset_adults_rsv_further_s3_sensitive_sensitivity analyse_dataset_adults_flu_s3_sensitive_sensitivity analyse_dataset_adults_flu_further_s3_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_s3_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_further_s3_sensitive_sensitivity process_dataset_adults_s4_sensitive_sensitivity describe_dataset_adults_s4_sensitive_sensitivity analyse_dataset_adults_rsv_s4_sensitive_sensitivity analyse_dataset_adults_rsv_further_s4_sensitive_sensitivity analyse_dataset_adults_flu_s4_sensitive_sensitivity 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analyse_dataset_infants_covid_full_s5_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_s5_sensitive_sensitivity analyse_dataset_infantsfurther__covid_ses_s5_sensitive_sensitivity analyse_dataset_infants_further_covid_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_ses_s5_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_further_covid_ses_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_further_covid_full_s5_sensitive_sensitivity process_dataset_infants_s6_sensitive_sensitivity describe_dataset_infants_s6_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_s6_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_s6_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_s6_sensitive_sensitivity analyse_dataset_infants_rsv_ses_s6_sensitive_sensitivity analyse_dataset_infants_flu_ses_s6_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_s6_sensitive_sensitivity analyse_dataset_infants_rsv_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_flu_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_rsv_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_flu_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_rsv_full_s6_sensitive_sensitivity analyse_dataset_infants_flu_full_s6_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_full_s6_sensitive_sensitivity analyse_dataset_infants_further_rsv_ethnicity_s6_sensitive_sensitivity analyse_dataset_infants_further_flu_ethnicity_s6_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_sensitive_sensitivity analyse_dataset_infants_further_rsv_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_flu_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_rsv_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_flu_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_rsv_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_flu_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_rsv_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_flu_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_rsv_full_s6_sensitive_sensitivity analyse_dataset_infants_further_flu_full_s6_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_full_s6_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_s6_sensitive_sensitivity analyse_dataset_infants_covid_ses_s6_sensitive_sensitivity analyse_dataset_infants_covid_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_covid_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_covid_full_s6_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_s6_sensitive_sensitivity analyse_dataset_infantsfurther__covid_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_covid_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_ses_s6_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_covid_ses_hh_comp_s6_sensitive_sensitivity analyse_dataset_infants_further_covid_full_s6_sensitive_sensitivity process_dataset_infants_s7_sensitive_sensitivity describe_dataset_infants_s7_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_s7_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_s7_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_s7_sensitive_sensitivity analyse_dataset_infants_rsv_ses_s7_sensitive_sensitivity analyse_dataset_infants_flu_ses_s7_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_s7_sensitive_sensitivity analyse_dataset_infants_rsv_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_flu_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_rsv_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_flu_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_rsv_full_s7_sensitive_sensitivity analyse_dataset_infants_flu_full_s7_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_full_s7_sensitive_sensitivity analyse_dataset_infants_further_rsv_ethnicity_s7_sensitive_sensitivity analyse_dataset_infants_further_flu_ethnicity_s7_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_sensitive_sensitivity analyse_dataset_infants_further_rsv_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_flu_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_rsv_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_flu_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_rsv_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_flu_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_rsv_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_flu_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_rsv_full_s7_sensitive_sensitivity analyse_dataset_infants_further_flu_full_s7_sensitive_sensitivity analyse_dataset_infants_further_overall_and_all_cause_full_s7_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_s7_sensitive_sensitivity analyse_dataset_infants_covid_ses_s7_sensitive_sensitivity analyse_dataset_infants_covid_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_covid_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_covid_full_s7_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_s7_sensitive_sensitivity analyse_dataset_infantsfurther__covid_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_covid_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_ses_s7_sensitive_sensitivity analyse_dataset_infants_further_covid_ethnicity_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_covid_ses_hh_comp_s7_sensitive_sensitivity analyse_dataset_infants_further_covid_full_s7_sensitive_sensitivity -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_specific_secondary_older_adults collate_rates_tables_specific_sensitivity_older_adults collate_rates_tables_sensitive_sensitivity_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_outputs_tables_older_adults_sensitivity collate_flu_outputs_tables_older_adults_sensitivity collate_covid_outputs_tables_older_adults_sensitivity collate_overall_and_all_cause_outputs_tables_older_adults_sensitivity collate_flow_chart_tables_adults collate_table1_tables_adults collate_rates_tables_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_specific_secondary_adults collate_rates_tables_specific_sensitivity_adults collate_rates_tables_sensitive_sensitivity_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_outputs_tables_adults_sensitivity collate_flu_outputs_tables_adults_sensitivity collate_covid_outputs_tables_adults_sensitivity collate_overall_and_all_cause_outputs_tables_adults_sensitivity 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_specific_secondary_children_and_adolescents collate_rates_tables_specific_sensitivity_children_and_adolescents collate_rates_tables_sensitive_sensitivity_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_outputs_tables_children_and_adolescents_sensitivity collate_flu_outputs_tables_children_and_adolescents_sensitivity collate_covid_outputs_tables_children_and_adolescents_sensitivity collate_overall_and_all_cause_outputs_tables_children_and_adolescents_sensitivity collate_flow_chart_tables_infants collate_table1_tables_infants collate_rates_tables_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_specific_secondary_infants collate_rates_tables_specific_sensitivity_infants collate_rates_tables_sensitive_sensitivity_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_phenotype_sensitivity_tables_infants collate_rsv_model_outputs_tables_infants_sensitivity collate_flu_model_outputs_tables_infants_sensitivity collate_covid_model_outputs_tables_infants_sensitivity collate_overall_and_all_cause_model_outputs_tables_infants_sensitivity +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_specific_secondary_older_adults collate_rates_tables_specific_sensitivity_older_adults collate_rates_tables_sensitive_sensitivity_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_outputs_tables_older_adults collate_rsv_outputs_tables_older_adults_secondary collate_flu_outputs_tables_older_adults_secondary collate_covid_outputs_tables_older_adults_secondary collate_overall_and_all_cause_outputs_tables_older_adults_secondary collate_rsv_outputs_tables_older_adults_sensitivity collate_flu_outputs_tables_older_adults_sensitivity collate_covid_outputs_tables_older_adults_sensitivity collate_overall_and_all_cause_outputs_tables_older_adults_sensitivity collate_flow_chart_tables_adults collate_table1_tables_adults collate_rates_tables_specific_primary_adults collate_rates_tables_sensitive_primary_adults collate_rates_tables_specific_secondary_adults collate_rates_tables_specific_sensitivity_adults collate_rates_tables_sensitive_sensitivity_adults collate_rsv_model_outputs_tables_adults collate_flu_model_outputs_tables_adults collate_covid_model_outputs_tables_adults collate_overall_and_all_cause_outputs_tables_adults collate_rsv_outputs_tables_adults_secondary collate_flu_outputs_tables_adults_secondary collate_covid_outputs_tables_adults_secondary collate_overall_and_all_cause_outputs_tables_adults_secondary collate_rsv_outputs_tables_adults_sensitivity collate_flu_outputs_tables_adults_sensitivity collate_covid_outputs_tables_adults_sensitivity collate_overall_and_all_cause_outputs_tables_adults_sensitivity 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_specific_secondary_children_and_adolescents collate_rates_tables_specific_sensitivity_children_and_adolescents collate_rates_tables_sensitive_sensitivity_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_outputs_tables_children_and_adolescents collate_rsv_outputs_tables_children_and_adolescents_secondary collate_flu_outputs_tables_children_and_adolescents_secondary collate_covid_outputs_tables_children_and_adolescents_secondary collate_overall_and_all_cause_outputs_tables_children_and_adolescents_secondary collate_rsv_outputs_tables_children_and_adolescents_sensitivity collate_flu_outputs_tables_children_and_adolescents_sensitivity collate_covid_outputs_tables_children_and_adolescents_sensitivity collate_overall_and_all_cause_outputs_tables_children_and_adolescents_sensitivity collate_flow_chart_tables_infants collate_table1_tables_infants collate_rates_tables_specific_primary_infants collate_rates_tables_sensitive_primary_infants collate_rates_tables_specific_secondary_infants collate_rates_tables_specific_sensitivity_infants collate_rates_tables_sensitive_sensitivity_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_model_outputs_tables_infants_secondary collate_flu_model_outputs_tables_infants_secondary collate_covid_model_outputs_tables_infants_secondary collate_overall_and_all_cause_model_outputs_tables_infants_secondary collate_phenotype_sensitivity_tables_infants collate_rsv_model_outputs_tables_infants_sensitivity collate_flu_model_outputs_tables_infants_sensitivity collate_covid_model_outputs_tables_infants_sensitivity collate_overall_and_all_cause_model_outputs_tables_infants_sensitivity diff --git a/create-project.R b/create-project.R index 6651ee1..172ecca 100644 --- a/create-project.R +++ b/create-project.R @@ -722,6 +722,7 @@ action_covid <- function(cohort, season, dates, codelist_type, moderately_sensitive = lst( csv = glue("output/results/models/further_covid_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), ) + ) } @@ -739,137 +740,1298 @@ action_covid_infants <- function(cohort, season, dates, codelist_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")), + 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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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/outcome_covid/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")), + ) + + ) + +} + +##secondary analysis actions + +action_secondary_rsv <- function(cohort, season, dates, codelist_type, + investigation_type, season_start_date, + season_end_date) { + + splice( + + action( + name = glue("process_dataset_{cohort}_s2_specific_secondary"), + run = glue("r:latest analysis/secondary_analyses/data_processing_sec.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}_s2_specific_secondary"), + glue("process_household_information_s2")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_s2_specific_secondary.arrow"), + ) + ), + + action( + name = glue("describe_dataset_{cohort}_s2_specific_secondary"), + 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}_s2_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/rates/rates_{cohort}_s2_specific_secondary.csv"), + ) + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/rsv_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv")) + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_further_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/further_rsv_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv")) + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_further_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) + + ) + + ) + +} + +action_secondary_flu <- function(cohort, season, dates, codelist_type, + investigation_type, season_start_date, + season_end_date) { + + splice( + + action( + name = glue("process_dataset_{cohort}_s3_specific_secondary"), + run = glue("r:latest analysis/secondary_analyses/data_processing_sec.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}_s3_specific_secondary"), + glue("process_household_information_s3")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_s3_specific_secondary.arrow"), + ) + ), + + action( + name = glue("describe_dataset_{cohort}_s3_specific_secondary"), + 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}_s3_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/rates/rates_{cohort}_s3_specific_secondary.csv"), + ) + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/flu_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv")) + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_further_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/further_flu_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv")) + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_further_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) + + ) + + ) + +} + +action_secondary_covid <- function(cohort, season, dates, codelist_type, + investigation_type, season_start_date, season_end_date) { + + splice( + + action( + name = glue("process_dataset_{cohort}_s5_specific_secondary"), + run = glue("r:latest analysis/secondary_analyses/data_processing_sec.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}_s5_specific_secondary"), + glue("process_household_information_s5")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_s5_specific_secondary.arrow"), + ) + ), + + action( + name = glue("describe_dataset_{cohort}_s5_specific_secondary"), + 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}_s5_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/rates/rates_{cohort}_s5_specific_secondary.csv"), + ) + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_covid/covid_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_further_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_covid/further_covid_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_covid_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_further_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ) + + ) + +} + +action_secondary_rsv_infants <- function(cohort, season, dates, codelist_type, + investigation_type, season_start_date, + season_end_date) { + + splice( + + action( + name = glue("process_dataset_{cohort}_s2_specific_secondary"), + run = glue("r:latest analysis/secondary_analyses/data_processing_sec.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}_s2_specific_secondary"), + glue("process_household_information_s2")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_s2_specific_secondary.arrow"), + ) + ), + + action( + name = glue("describe_dataset_{cohort}_s2_specific_secondary"), + 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}_s2_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/rates/rates_{cohort}_s2_specific_secondary.csv"), + ) + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_rsv_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/rsv_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_rsv_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_rsv/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_rsv_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/further_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ) + + ) + +} + +action_secondary_flu_infants <- function(cohort, season, dates, codelist_type, + investigation_type, season_start_date, + season_end_date) { + + splice( + + action( + name = glue("process_dataset_{cohort}_s3_specific_secondary"), + run = glue("r:latest analysis/secondary_analyses/data_processing_sec.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}_s3_specific_secondary"), + glue("process_household_information_s3")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_s3_specific_secondary.arrow"), + ) + ), + + action( + name = glue("describe_dataset_{cohort}_s3_specific_secondary"), + 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}_s3_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/rates/rates_{cohort}_s3_specific_secondary.csv"), + ) + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_flu_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/flu_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_flu_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_flu/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_flu_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/further_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ) + + ) + +} + +action_secondary_covid_infants <- function(cohort, season, dates, codelist_type, + investigation_type, season_start_date, + season_end_date) { + + splice( + + action( + name = glue("process_dataset_{cohort}_s5_specific_secondary"), + run = glue("r:latest analysis/secondary_analyses/data_processing_sec.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}_s5_specific_secondary"), + glue("process_household_information_s5")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_s5_specific_secondary.arrow"), + ) + ), + + action( + name = glue("describe_dataset_{cohort}_s5_specific_secondary"), + 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}_s5_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/rates/rates_{cohort}_s5_specific_secondary.csv"), + ) + ), + + action( + name = glue("analyse_dataset_{cohort}_covid_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_covid/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/covid_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_covid_ses_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_covid_ses_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/covid_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/covid_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_covid_hh_comp_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_covid_hh_comp_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/covid_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/covid_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_covid_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_covid_ethnicity_ses_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/covid_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/covid_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_covid_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_covid_ses_hh_comp_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/covid_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/covid_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_covid_full_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_covid_full_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/covid_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/covid_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/further_covid_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}further__covid_ses_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}further__covid_ses_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/further_covid_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_further_covid_hh_comp_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_further_covid_hh_comp_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/further_covid_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_ses_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/further_covid_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_hh_comp_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/further_covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_further_covid_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_further_covid_ses_hh_comp_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/further_covid_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), action( - name = glue("analyse_dataset_{cohort}_further_covid_full_{season}_{codelist_type}_{investigation_type}"), + name = glue("analyse_dataset_{cohort}_further_covid_full_{season}_specific_secondary"), run = glue("r:latest analysis/outcome_covid/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}")), + needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), + csv = glue("output/results/models/further_covid_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_overall_and_all_cause_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/overall_and_all_cause_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}further__overall_and_all_cause_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_ses_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_hh_comp_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_specific_secondary.csv")), + ), + + action( + name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_full_{season}_specific_secondary"), + run = glue("r:latest analysis/outcome_overall_and_all_cause/further_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}_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/results/models/further_overall_and_all_cause_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ) ) @@ -884,12 +2046,38 @@ action_descriptive <- function(cohort, season, dates, codelist_type, splice( + action( + name = glue("generate_dataset_{cohort}_{season}_specific_secondary"), + run = glue("ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_{cohort}_{dates}_specific_secondary.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}_specific_secondary.arrow"), + ) + ), + + action( + name = glue("process_cohort_{cohort}_{season}_specific_secondary"), + 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}_specific_secondary"), + glue("process_household_information_{season}")), + highly_sensitive = lst( + cohort = glue("output/data/input_processed_{cohort}_{dates}_specific_secondary.arrow"), + ) + ), + action( name = glue("describe_cohort_{cohort}_{season}"), run = glue("r:latest analysis/cohort_description.R {cohort} {season_start_date} {season_end_date} specific secondary"), arguments = c(cohort, season, dates, codelist_type, investigation_type, season_start_date, season_end_date), - needs = list(glue("process_dataset_{cohort}_{season}_specific_secondary")), + needs = list(glue("process_cohort_{cohort}_{season}_specific_secondary")), moderately_sensitive = lst( csv = glue("output/table1/table1_{cohort}_{dates}.csv")), ) @@ -1708,13 +2896,9 @@ action_finalise <- function(cohort) { name = glue("collate_rates_tables_specific_secondary_{cohort}"), run = glue("r:latest analysis/collation_code/rates_table_specific_secondary_collation.R {cohort}"), arguments = c(cohort), - needs = list(glue("describe_dataset_{cohort}_s1_specific_secondary"), - glue("describe_dataset_{cohort}_s2_specific_secondary"), + needs = list(glue("describe_dataset_{cohort}_s2_specific_secondary"), glue("describe_dataset_{cohort}_s3_specific_secondary"), - glue("describe_dataset_{cohort}_s4_specific_secondary"), - glue("describe_dataset_{cohort}_s5_specific_secondary"), - glue("describe_dataset_{cohort}_s6_specific_secondary"), - glue("describe_dataset_{cohort}_s7_specific_secondary")), + glue("describe_dataset_{cohort}_s5_specific_secondary")), moderately_sensitive = lst( csv = glue("output/collated/descriptive/{cohort}_rates_specific_secondary_collated.csv")) ), @@ -1813,7 +2997,7 @@ action_finalise <- function(cohort) { ), action( - name = glue("collate_overall_and_all_cause_model_outputs_tables_{cohort}"), + name = glue("collate_overall_and_all_cause_outputs_tables_{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_s1_specific_primary"), @@ -1834,6 +3018,42 @@ action_finalise <- function(cohort) { csv = glue("output/collated/analytic/{cohort}_overall_and_all_cause_model_outputs_collated.csv")) ), + action( + name = glue("collate_rsv_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/rsv_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_rsv_s2_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/secondary/{cohort}_rsv_model_outputs_collated_secondary.csv")) + ), + + action( + name = glue("collate_flu_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/flu_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_flu_s3_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/secondary/{cohort}_flu_model_outputs_collated_secondary.csv")) + ), + + action( + name = glue("collate_covid_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/covid_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_covid_s5_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/secondary/{cohort}_covid_model_outputs_collated_secondary.csv")) + ), + + action( + name = glue("collate_overall_and_all_cause_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/overall_and_all_cause_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_overall_and_all_cause_s5_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/secondary/{cohort}_overall_and_all_cause_model_outputs_collated_secondary.csv")) + ), + action( name = glue("collate_rsv_outputs_tables_{cohort}_sensitivity"), run = glue("r:latest analysis/collation_code/rsv_outputs_table_collation_sensitivity.R {cohort}"), @@ -1853,7 +3073,7 @@ action_finalise <- function(cohort) { glue("analyse_dataset_{cohort}_rsv_s6_sensitive_sensitivity"), glue("analyse_dataset_{cohort}_rsv_s7_sensitive_sensitivity")), moderately_sensitive = lst( - csv = glue("output/collated/analytic/{cohort}_rsv_model_outputs_collated_sensitivity.csv")) + csv = glue("output/collated/analytic/sensitivity/{cohort}_rsv_model_outputs_collated_sensitivity.csv")) ), action( @@ -1875,7 +3095,7 @@ action_finalise <- function(cohort) { glue("analyse_dataset_{cohort}_flu_s6_sensitive_sensitivity"), glue("analyse_dataset_{cohort}_flu_s7_sensitive_sensitivity")), moderately_sensitive = lst( - csv = glue("output/collated/analytic/{cohort}_flu_model_outputs_collated_sensitivity.csv")) + csv = glue("output/collated/analytic/sensitivity/{cohort}_flu_model_outputs_collated_sensitivity.csv")) ), action( @@ -1891,7 +3111,7 @@ action_finalise <- function(cohort) { glue("analyse_dataset_{cohort}_covid_s6_sensitive_sensitivity"), glue("analyse_dataset_{cohort}_covid_s7_sensitive_sensitivity")), moderately_sensitive = lst( - csv = glue("output/collated/analytic/{cohort}_covid_model_outputs_collated_sensitivity.csv")) + csv = glue("output/collated/analytic/sensitivity/{cohort}_covid_model_outputs_collated_sensitivity.csv")) ), action( @@ -1913,7 +3133,7 @@ action_finalise <- function(cohort) { glue("analyse_dataset_{cohort}_overall_and_all_cause_s6_sensitive_sensitivity"), glue("analyse_dataset_{cohort}_overall_and_all_cause_s7_sensitive_sensitivity")), moderately_sensitive = lst( - csv = glue("output/collated/analytic/{cohort}_overall_and_all_cause_model_outputs_collated_sensitivity.csv")) + csv = glue("output/collated/analytic/sensitivity/{cohort}_overall_and_all_cause_model_outputs_collated_sensitivity.csv")) ) ) @@ -1988,13 +3208,9 @@ action_finalise_infants <- function(cohort) { name = glue("collate_rates_tables_specific_secondary_{cohort}"), run = glue("r:latest analysis/collation_code/rates_table_specific_secondary_collation.R {cohort}"), arguments = c(cohort), - needs = list(glue("describe_dataset_{cohort}_s1_specific_secondary"), - glue("describe_dataset_{cohort}_s2_specific_secondary"), + needs = list(glue("describe_dataset_{cohort}_s2_specific_secondary"), glue("describe_dataset_{cohort}_s3_specific_secondary"), - glue("describe_dataset_{cohort}_s4_specific_secondary"), - glue("describe_dataset_{cohort}_s5_specific_secondary"), - glue("describe_dataset_{cohort}_s6_specific_secondary"), - glue("describe_dataset_{cohort}_s7_specific_secondary")), + glue("describe_dataset_{cohort}_s5_specific_secondary")), moderately_sensitive = lst( csv = glue("output/collated/descriptive/{cohort}_rates_specific_secondary_collated.csv")) ), @@ -2411,6 +3627,66 @@ action_finalise_infants <- function(cohort) { csv = glue("output/collated/analytic/{cohort}_overall_and_all_cause_model_outputs_collated.csv")) ), + action( + name = glue("collate_rsv_model_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/rsv_model_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_rsv_ethnicity_s2_specific_secondary"), + glue("analyse_dataset_{cohort}_rsv_ses_s2_specific_secondary"), + glue("analyse_dataset_{cohort}_rsv_hh_comp_s2_specific_secondary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_ses_s2_specific_secondary"), + glue("analyse_dataset_{cohort}_rsv_ethnicity_hh_comp_s2_specific_secondary"), + glue("analyse_dataset_{cohort}_rsv_ses_hh_comp_s2_specific_secondary"), + glue("analyse_dataset_{cohort}_rsv_full_s2_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/{cohort}_rsv_model_outputs_secondary_collated.csv")) + ), + + action( + name = glue("collate_flu_model_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/flu_model_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_flu_ethnicity_s3_specific_secondary"), + glue("analyse_dataset_{cohort}_flu_ses_s3_specific_secondary"), + glue("analyse_dataset_{cohort}_flu_hh_comp_s3_specific_secondary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_ses_s3_specific_secondary"), + glue("analyse_dataset_{cohort}_flu_ethnicity_hh_comp_s3_specific_secondary"), + glue("analyse_dataset_{cohort}_flu_ses_hh_comp_s3_specific_secondary"), + glue("analyse_dataset_{cohort}_flu_full_s3_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/{cohort}_flu_model_outputs_secondary_collated.csv")) + ), + + action( + name = glue("collate_covid_model_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/covid_model_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_covid_ethnicity_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_covid_ses_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_covid_hh_comp_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_ses_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_covid_ethnicity_hh_comp_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_covid_ses_hh_comp_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_covid_full_s5_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/{cohort}_covid_model_outputs_secondary_collated.csv")) + ), + + action( + name = glue("collate_overall_and_all_cause_model_outputs_tables_{cohort}_secondary"), + run = glue("r:latest analysis/collation_code/overall_and_all_cause_model_outputs_table_collation_secondary.R {cohort}"), + arguments = c(cohort), + needs = list(glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_hh_comp_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_ses_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ethnicity_hh_comp_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_ses_hh_comp_s5_specific_secondary"), + glue("analyse_dataset_{cohort}_overall_and_all_cause_full_s5_specific_secondary")), + moderately_sensitive = lst( + csv = glue("output/collated/analytic/{cohort}_overall_and_all_cause_model_outputs_secondary_collated.csv")) + ), + action( name = glue("collate_phenotype_sensitivity_tables_{cohort}"), run = glue("r:latest analysis/collation_code/phenotype_sensitivity_table_collation.R {cohort}"), @@ -3008,64 +4284,6 @@ actions_list <- splice( action_specified_infants("infants", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), action_covid_infants("infants", "s7", "2022_2023", "sensitive", "primary", "season7_start_date", "season7_end_date"), - comment("# # # # # # # # # # # # # # # # # # #", "SECONDARY ANALYSES", "# # # # # # # # # # # # # # # # # # #"), - - comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), - - action_specified("older_adults", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), - action_specified("older_adults", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), - action_specified("older_adults", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), - action_specified("older_adults", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_covid("older_adults", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_specified("older_adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_covid("older_adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_specified("older_adults", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_covid("older_adults", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_specified("older_adults", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - action_covid("older_adults", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - - comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Adults, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), - - action_specified("adults", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), - action_specified("adults", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), - action_specified("adults", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), - action_specified("adults", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_covid("adults", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_specified("adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_covid("adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_specified("adults", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_covid("adults", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_specified("adults", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - action_covid("adults", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - - comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Children and Adolescents, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), - - action_specified("children_and_adolescents", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), - action_specified("children_and_adolescents", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), - action_specified("children_and_adolescents", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), - action_specified("children_and_adolescents", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_covid("children_and_adolescents", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_specified("children_and_adolescents", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_covid("children_and_adolescents", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_specified("children_and_adolescents", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_covid("children_and_adolescents", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_specified("children_and_adolescents", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - action_covid("children_and_adolescents", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - - comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Infants, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), - - action_specified("infants", "s1", "2016_2017", "specific", "secondary", "season1_start_date", "season1_end_date"), - action_specified("infants", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), - action_specified("infants", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), - action_specified("infants", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_covid("infants", "s4", "2019_2020", "specific", "secondary", "season4_start_date", "season4_end_date"), - action_specified("infants", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_covid("infants", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), - action_specified("infants", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_covid("infants", "s6", "2021_2022", "specific", "secondary", "season6_start_date", "season6_end_date"), - action_specified("infants", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - action_covid("infants", "s7", "2022_2023", "specific", "secondary", "season7_start_date", "season7_end_date"), - comment("# # # # # # # # # # # # # # # # # # #", "DESCRIPTIVE ANALYSES", "# # # # # # # # # # # # # # # # # # #"), comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults", "# # # # # # # # # # # # # # # # # # #"), @@ -3108,6 +4326,32 @@ actions_list <- splice( 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("# # # # # # # # # # # # # # # # # # #", "SECONDARY ANALYSES", "# # # # # # # # # # # # # # # # # # #"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_secondary_rsv("older_adults", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_secondary_flu("older_adults", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_secondary_covid("older_adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Adults, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_secondary_rsv("adults", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_secondary_flu("adults", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_secondary_covid("adults", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Children and Adolescents, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_secondary_rsv("children_and_adolescents", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_secondary_flu("children_and_adolescents", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_secondary_covid("children_and_adolescents", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + + comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Infants, Codelist Type: Specific, Investigation Type: Secondary", "# # # # # # # # # # # # # # # # # # #"), + + action_secondary_rsv_infants("infants", "s2", "2017_2018", "specific", "secondary", "season2_start_date", "season2_end_date"), + action_secondary_flu_infants("infants", "s3", "2018_2019", "specific", "secondary", "season3_start_date", "season3_end_date"), + action_secondary_covid_infants("infants", "s5", "2020_2021", "specific", "secondary", "season5_start_date", "season5_end_date"), + comment("# # # # # # # # # # # # # # # # # # #", "EXPLORATORY ANALYSES", "# # # # # # # # # # # # # # # # # # #"), comment("# # # # # # # # # # # # # # # # # # #", "Cohort: Older Adults", "# # # # # # # # # # # # # # # # # # #"), @@ -3328,7 +4572,7 @@ names(actions_list) %>% tibble(action=.) %>% actions_list %>% names() %>% - str_subset("^process_") %>% + str_subset("^generate.+secondary$") %>% tibble(action=.) %>% mutate( model = action=="" & lag(action!="", 1, TRUE), diff --git a/project.yaml b/project.yaml index 7d8ef96..11e3299 100644 --- a/project.yaml +++ b/project.yaml @@ -12405,12 +12405,10 @@ actions: csv: output/results/models/further_covid_full_model_outputs_infants_2022_2023_sensitive_primary.csv ## # # # # # # # # # # # # # # # # # # # - ## SECONDARY ANALYSES + ## DESCRIPTIVE ANALYSES ## # # # # # # # # # # # # # # # # # # # ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Older Adults, Codelist Type: Specific, Investigation Type: Secondary - - + ## Cohort: Older Adults ## # # # # # # # # # # # # # # # # # # # generate_dataset_older_adults_s1_specific_secondary: @@ -12423,7 +12421,7 @@ actions: highly_sensitive: dataset: output/data/input_older_adults_2016_2017_specific_secondary.arrow - process_dataset_older_adults_s1_specific_secondary: + process_cohort_older_adults_s1_specific_secondary: run: r:latest analysis/data_processing.R older_adults season1_start_date season1_end_date specific secondary older_adults s1 2016_2017 specific secondary season1_start_date season1_end_date @@ -12434,75 +12432,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_older_adults_2016_2017_specific_secondary.arrow - describe_dataset_older_adults_s1_specific_secondary: - run: r:latest analysis/report.R older_adults season1_start_date season1_end_date + describe_cohort_older_adults_s1: + run: r:latest analysis/cohort_description.R older_adults season1_start_date season1_end_date specific secondary older_adults s1 2016_2017 specific secondary season1_start_date season1_end_date needs: - - process_dataset_older_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_older_adults_2016_2017_specific_secondary.csv - - analyse_dataset_older_adults_rsv_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season1_start_date - season1_end_date specific secondary older_adults s1 2016_2017 specific secondary - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_older_adults_2016_2017_specific_*.csv - - analyse_dataset_older_adults_rsv_further_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season1_start_date - season1_end_date specific secondary older_adults s1 2016_2017 specific secondary - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_older_adults_2016_2017_specific_*.csv - - analyse_dataset_older_adults_flu_s1_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R older_adults season1_start_date - season1_end_date specific secondary older_adults s1 2016_2017 specific secondary - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_older_adults_2016_2017_specific_*.csv - - analyse_dataset_older_adults_flu_further_s1_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season1_start_date - season1_end_date specific secondary older_adults s1 2016_2017 specific secondary - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_older_adults_2016_2017_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_s1_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - older_adults season1_start_date season1_end_date specific secondary older_adults - s1 2016_2017 specific secondary season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2016_2017_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_further_s1_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - older_adults season1_start_date season1_end_date specific secondary older_adults - s1 2016_2017 specific secondary season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_secondary + - process_cohort_older_adults_s1_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2016_2017_specific_*.csv + csv: output/table1/table1_older_adults_2016_2017.csv generate_dataset_older_adults_s2_specific_secondary: run: |- @@ -12514,7 +12452,7 @@ actions: highly_sensitive: dataset: output/data/input_older_adults_2017_2018_specific_secondary.arrow - process_dataset_older_adults_s2_specific_secondary: + process_cohort_older_adults_s2_specific_secondary: run: r:latest analysis/data_processing.R older_adults season2_start_date season2_end_date specific secondary older_adults s2 2017_2018 specific secondary season2_start_date season2_end_date @@ -12525,75 +12463,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_older_adults_2017_2018_specific_secondary.arrow - describe_dataset_older_adults_s2_specific_secondary: - run: r:latest analysis/report.R older_adults season2_start_date season2_end_date + describe_cohort_older_adults_s2: + run: r:latest analysis/cohort_description.R older_adults season2_start_date season2_end_date specific secondary older_adults s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - - process_dataset_older_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_older_adults_2017_2018_specific_secondary.csv - - analyse_dataset_older_adults_rsv_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season2_start_date - season2_end_date specific secondary older_adults s2 2017_2018 specific secondary - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_older_adults_2017_2018_specific_*.csv - - analyse_dataset_older_adults_rsv_further_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season2_start_date - season2_end_date specific secondary older_adults s2 2017_2018 specific secondary - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_older_adults_2017_2018_specific_*.csv - - analyse_dataset_older_adults_flu_s2_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R older_adults season2_start_date - season2_end_date specific secondary older_adults s2 2017_2018 specific secondary - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_older_adults_2017_2018_specific_*.csv - - analyse_dataset_older_adults_flu_further_s2_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season2_start_date - season2_end_date specific secondary older_adults s2 2017_2018 specific secondary - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_older_adults_2017_2018_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - older_adults season2_start_date season2_end_date specific secondary older_adults - s2 2017_2018 specific secondary season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2017_2018_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_further_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - older_adults season2_start_date season2_end_date specific secondary older_adults - s2 2017_2018 specific secondary season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_secondary + - process_cohort_older_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2017_2018_specific_*.csv + csv: output/table1/table1_older_adults_2017_2018.csv generate_dataset_older_adults_s3_specific_secondary: run: |- @@ -12605,7 +12483,7 @@ actions: highly_sensitive: dataset: output/data/input_older_adults_2018_2019_specific_secondary.arrow - process_dataset_older_adults_s3_specific_secondary: + process_cohort_older_adults_s3_specific_secondary: run: r:latest analysis/data_processing.R older_adults season3_start_date season3_end_date specific secondary older_adults s3 2018_2019 specific secondary season3_start_date season3_end_date @@ -12616,75 +12494,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_older_adults_2018_2019_specific_secondary.arrow - describe_dataset_older_adults_s3_specific_secondary: - run: r:latest analysis/report.R older_adults season3_start_date season3_end_date + describe_cohort_older_adults_s3: + run: r:latest analysis/cohort_description.R older_adults season3_start_date season3_end_date specific secondary older_adults s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_older_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_older_adults_2018_2019_specific_secondary.csv - - analyse_dataset_older_adults_rsv_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season3_start_date - season3_end_date specific secondary older_adults s3 2018_2019 specific secondary - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_older_adults_2018_2019_specific_*.csv - - analyse_dataset_older_adults_rsv_further_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season3_start_date - season3_end_date specific secondary older_adults s3 2018_2019 specific secondary - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_older_adults_2018_2019_specific_*.csv - - analyse_dataset_older_adults_flu_s3_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R older_adults season3_start_date - season3_end_date specific secondary older_adults s3 2018_2019 specific secondary - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_older_adults_2018_2019_specific_*.csv - - analyse_dataset_older_adults_flu_further_s3_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season3_start_date - season3_end_date specific secondary older_adults s3 2018_2019 specific secondary - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_older_adults_2018_2019_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - older_adults season3_start_date season3_end_date specific secondary older_adults - s3 2018_2019 specific secondary season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2018_2019_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_further_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - older_adults season3_start_date season3_end_date specific secondary older_adults - s3 2018_2019 specific secondary season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_secondary + - process_cohort_older_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2018_2019_specific_*.csv + csv: output/table1/table1_older_adults_2018_2019.csv generate_dataset_older_adults_s4_specific_secondary: run: |- @@ -12696,7 +12514,7 @@ actions: highly_sensitive: dataset: output/data/input_older_adults_2019_2020_specific_secondary.arrow - process_dataset_older_adults_s4_specific_secondary: + process_cohort_older_adults_s4_specific_secondary: run: r:latest analysis/data_processing.R older_adults season4_start_date season4_end_date specific secondary older_adults s4 2019_2020 specific secondary season4_start_date season4_end_date @@ -12707,95 +12525,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_older_adults_2019_2020_specific_secondary.arrow - describe_dataset_older_adults_s4_specific_secondary: - run: r:latest analysis/report.R older_adults season4_start_date season4_end_date + describe_cohort_older_adults_s4: + run: r:latest analysis/cohort_description.R older_adults season4_start_date season4_end_date specific secondary older_adults s4 2019_2020 specific secondary season4_start_date season4_end_date needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_older_adults_2019_2020_specific_secondary.csv - - analyse_dataset_older_adults_rsv_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season4_start_date - season4_end_date specific secondary older_adults s4 2019_2020 specific secondary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_older_adults_2019_2020_specific_*.csv - - analyse_dataset_older_adults_rsv_further_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season4_start_date - season4_end_date specific secondary older_adults s4 2019_2020 specific secondary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_older_adults_2019_2020_specific_*.csv - - analyse_dataset_older_adults_flu_s4_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R older_adults season4_start_date - season4_end_date specific secondary older_adults s4 2019_2020 specific secondary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_older_adults_2019_2020_specific_*.csv - - analyse_dataset_older_adults_flu_further_s4_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season4_start_date - season4_end_date specific secondary older_adults s4 2019_2020 specific secondary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_older_adults_2019_2020_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_s4_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - older_adults season4_start_date season4_end_date specific secondary older_adults - s4 2019_2020 specific secondary season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2019_2020_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_further_s4_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - older_adults season4_start_date season4_end_date specific secondary older_adults - s4 2019_2020 specific secondary season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2019_2020_specific_*.csv - - analyse_dataset_older_adults_covid_s4_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R older_adults season4_start_date - season4_end_date specific secondary older_adults s4 2019_2020 specific secondary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_older_adults_2019_2020_specific_secondary.csv - - analyse_dataset_older_adults_covid_further_s4_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R older_adults season4_start_date - season4_end_date specific secondary older_adults s4 2019_2020 specific secondary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_secondary + - process_cohort_older_adults_s4_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_older_adults_2019_2020_specific_secondary.csv + csv: output/table1/table1_older_adults_2019_2020.csv generate_dataset_older_adults_s5_specific_secondary: run: |- @@ -12807,7 +12545,7 @@ actions: highly_sensitive: dataset: output/data/input_older_adults_2020_2021_specific_secondary.arrow - process_dataset_older_adults_s5_specific_secondary: + process_cohort_older_adults_s5_specific_secondary: run: r:latest analysis/data_processing.R older_adults season5_start_date season5_end_date specific secondary older_adults s5 2020_2021 specific secondary season5_start_date season5_end_date @@ -12818,206 +12556,46 @@ actions: highly_sensitive: cohort: output/data/input_processed_older_adults_2020_2021_specific_secondary.arrow - describe_dataset_older_adults_s5_specific_secondary: - run: r:latest analysis/report.R older_adults season5_start_date season5_end_date + describe_cohort_older_adults_s5: + run: r:latest analysis/cohort_description.R older_adults season5_start_date season5_end_date specific secondary older_adults s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_older_adults_s5_specific_secondary + - process_cohort_older_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_older_adults_2020_2021_specific_secondary.csv + csv: output/table1/table1_older_adults_2020_2021.csv - analyse_dataset_older_adults_rsv_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season5_start_date - season5_end_date specific secondary older_adults s5 2020_2021 specific secondary - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_secondary + generate_dataset_older_adults_s6_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_older_adults_2021_2022_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_older_adults_2021_2022.arrow + -- older_adults season6_start_date season6_end_date specific secondary older_adults s6 2021_2022 specific secondary season6_start_date season6_end_date outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_older_adults_2020_2021_specific_*.csv + highly_sensitive: + dataset: output/data/input_older_adults_2021_2022_specific_secondary.arrow - analyse_dataset_older_adults_rsv_further_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season5_start_date - season5_end_date specific secondary older_adults s5 2020_2021 specific secondary - season5_start_date season5_end_date + process_cohort_older_adults_s6_specific_secondary: + run: r:latest analysis/data_processing.R older_adults season6_start_date season6_end_date + specific secondary older_adults s6 2021_2022 specific secondary season6_start_date + season6_end_date needs: - - process_dataset_older_adults_s5_specific_secondary + - generate_dataset_older_adults_s6_specific_secondary + - process_household_information_s6 outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_older_adults_2020_2021_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_older_adults_2021_2022_specific_secondary.arrow - analyse_dataset_older_adults_flu_s5_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R older_adults season5_start_date - season5_end_date specific secondary older_adults s5 2020_2021 specific secondary - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_older_adults_2020_2021_specific_*.csv - - analyse_dataset_older_adults_flu_further_s5_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season5_start_date - season5_end_date specific secondary older_adults s5 2020_2021 specific secondary - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_older_adults_2020_2021_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - older_adults season5_start_date season5_end_date specific secondary older_adults - s5 2020_2021 specific secondary season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2020_2021_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_further_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - older_adults season5_start_date season5_end_date specific secondary older_adults - s5 2020_2021 specific secondary season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2020_2021_specific_*.csv - - analyse_dataset_older_adults_covid_s5_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R older_adults season5_start_date - season5_end_date specific secondary older_adults s5 2020_2021 specific secondary - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_older_adults_2020_2021_specific_secondary.csv - - analyse_dataset_older_adults_covid_further_s5_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R older_adults season5_start_date - season5_end_date specific secondary older_adults s5 2020_2021 specific secondary - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_older_adults_2020_2021_specific_secondary.csv - - generate_dataset_older_adults_s6_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_older_adults_2021_2022_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_older_adults_2021_2022.arrow - -- older_adults season6_start_date season6_end_date specific secondary older_adults s6 2021_2022 specific secondary season6_start_date season6_end_date - outputs: - highly_sensitive: - dataset: output/data/input_older_adults_2021_2022_specific_secondary.arrow - - process_dataset_older_adults_s6_specific_secondary: - run: r:latest analysis/data_processing.R older_adults season6_start_date season6_end_date - specific secondary older_adults s6 2021_2022 specific secondary season6_start_date - season6_end_date - needs: - - generate_dataset_older_adults_s6_specific_secondary - - process_household_information_s6 - outputs: - highly_sensitive: - cohort: output/data/input_processed_older_adults_2021_2022_specific_secondary.arrow - - describe_dataset_older_adults_s6_specific_secondary: - run: r:latest analysis/report.R older_adults season6_start_date season6_end_date + describe_cohort_older_adults_s6: + run: r:latest analysis/cohort_description.R older_adults season6_start_date season6_end_date specific secondary older_adults s6 2021_2022 specific secondary season6_start_date season6_end_date needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_older_adults_2021_2022_specific_secondary.csv - - analyse_dataset_older_adults_rsv_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season6_start_date - season6_end_date specific secondary older_adults s6 2021_2022 specific secondary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_older_adults_2021_2022_specific_*.csv - - analyse_dataset_older_adults_rsv_further_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season6_start_date - season6_end_date specific secondary older_adults s6 2021_2022 specific secondary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_older_adults_2021_2022_specific_*.csv - - analyse_dataset_older_adults_flu_s6_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R older_adults season6_start_date - season6_end_date specific secondary older_adults s6 2021_2022 specific secondary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_older_adults_2021_2022_specific_*.csv - - analyse_dataset_older_adults_flu_further_s6_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season6_start_date - season6_end_date specific secondary older_adults s6 2021_2022 specific secondary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_older_adults_2021_2022_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - older_adults season6_start_date season6_end_date specific secondary older_adults - s6 2021_2022 specific secondary season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2021_2022_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_further_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - older_adults season6_start_date season6_end_date specific secondary older_adults - s6 2021_2022 specific secondary season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2021_2022_specific_*.csv - - analyse_dataset_older_adults_covid_s6_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R older_adults season6_start_date - season6_end_date specific secondary older_adults s6 2021_2022 specific secondary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_older_adults_2021_2022_specific_secondary.csv - - analyse_dataset_older_adults_covid_further_s6_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R older_adults season6_start_date - season6_end_date specific secondary older_adults s6 2021_2022 specific secondary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_secondary + - process_cohort_older_adults_s6_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_older_adults_2021_2022_specific_secondary.csv + csv: output/table1/table1_older_adults_2021_2022.csv generate_dataset_older_adults_s7_specific_secondary: run: |- @@ -13029,7 +12607,7 @@ actions: highly_sensitive: dataset: output/data/input_older_adults_2022_2023_specific_secondary.arrow - process_dataset_older_adults_s7_specific_secondary: + process_cohort_older_adults_s7_specific_secondary: run: r:latest analysis/data_processing.R older_adults season7_start_date season7_end_date specific secondary older_adults s7 2022_2023 specific secondary season7_start_date season7_end_date @@ -13040,98 +12618,18 @@ actions: highly_sensitive: cohort: output/data/input_processed_older_adults_2022_2023_specific_secondary.arrow - describe_dataset_older_adults_s7_specific_secondary: - run: r:latest analysis/report.R older_adults season7_start_date season7_end_date + describe_cohort_older_adults_s7: + run: r:latest analysis/cohort_description.R older_adults season7_start_date season7_end_date specific secondary older_adults s7 2022_2023 specific secondary season7_start_date season7_end_date needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_older_adults_2022_2023_specific_secondary.csv - - analyse_dataset_older_adults_rsv_s7_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season7_start_date - season7_end_date specific secondary older_adults s7 2022_2023 specific secondary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_older_adults_2022_2023_specific_*.csv - - analyse_dataset_older_adults_rsv_further_s7_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season7_start_date - season7_end_date specific secondary older_adults s7 2022_2023 specific secondary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_older_adults_2022_2023_specific_*.csv - - analyse_dataset_older_adults_flu_s7_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R older_adults season7_start_date - season7_end_date specific secondary older_adults s7 2022_2023 specific secondary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_older_adults_2022_2023_specific_*.csv - - analyse_dataset_older_adults_flu_further_s7_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season7_start_date - season7_end_date specific secondary older_adults s7 2022_2023 specific secondary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_older_adults_2022_2023_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - older_adults season7_start_date season7_end_date specific secondary older_adults - s7 2022_2023 specific secondary season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2022_2023_specific_*.csv - - analyse_dataset_older_adults_overall_and_all_cause_further_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - older_adults season7_start_date season7_end_date specific secondary older_adults - s7 2022_2023 specific secondary season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2022_2023_specific_*.csv - - analyse_dataset_older_adults_covid_s7_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R older_adults season7_start_date - season7_end_date specific secondary older_adults s7 2022_2023 specific secondary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_older_adults_2022_2023_specific_secondary.csv - - analyse_dataset_older_adults_covid_further_s7_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R older_adults season7_start_date - season7_end_date specific secondary older_adults s7 2022_2023 specific secondary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_secondary + - process_cohort_older_adults_s7_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_older_adults_2022_2023_specific_secondary.csv + csv: output/table1/table1_older_adults_2022_2023.csv ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Adults, Codelist Type: Specific, Investigation Type: Secondary + ## Cohort: Adults ## # # # # # # # # # # # # # # # # # # # generate_dataset_adults_s1_specific_secondary: @@ -13144,7 +12642,7 @@ actions: highly_sensitive: dataset: output/data/input_adults_2016_2017_specific_secondary.arrow - process_dataset_adults_s1_specific_secondary: + process_cohort_adults_s1_specific_secondary: run: r:latest analysis/data_processing.R adults season1_start_date season1_end_date specific secondary adults s1 2016_2017 specific secondary season1_start_date season1_end_date @@ -13155,74 +12653,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_adults_2016_2017_specific_secondary.arrow - describe_dataset_adults_s1_specific_secondary: - run: r:latest analysis/report.R adults season1_start_date season1_end_date specific - secondary adults s1 2016_2017 specific secondary season1_start_date season1_end_date - needs: - - process_dataset_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_adults_2016_2017_specific_secondary.csv - - analyse_dataset_adults_rsv_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R adults season1_start_date season1_end_date - specific secondary adults s1 2016_2017 specific secondary season1_start_date - season1_end_date - needs: - - process_dataset_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_adults_2016_2017_specific_*.csv - - analyse_dataset_adults_rsv_further_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season1_start_date - season1_end_date specific secondary adults s1 2016_2017 specific secondary season1_start_date - season1_end_date - needs: - - process_dataset_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_adults_2016_2017_specific_*.csv - - analyse_dataset_adults_flu_s1_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R adults season1_start_date season1_end_date + describe_cohort_adults_s1: + run: r:latest analysis/cohort_description.R adults season1_start_date season1_end_date specific secondary adults s1 2016_2017 specific secondary season1_start_date season1_end_date needs: - - process_dataset_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_adults_2016_2017_specific_*.csv - - analyse_dataset_adults_flu_further_s1_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R adults season1_start_date - season1_end_date specific secondary adults s1 2016_2017 specific secondary season1_start_date - season1_end_date - needs: - - process_dataset_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_adults_2016_2017_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_s1_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - adults season1_start_date season1_end_date specific secondary adults s1 2016_2017 - specific secondary season1_start_date season1_end_date - needs: - - process_dataset_adults_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_adults_2016_2017_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_further_s1_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - adults season1_start_date season1_end_date specific secondary adults s1 2016_2017 - specific secondary season1_start_date season1_end_date - needs: - - process_dataset_adults_s1_specific_secondary + - process_cohort_adults_s1_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2016_2017_specific_*.csv + csv: output/table1/table1_adults_2016_2017.csv generate_dataset_adults_s2_specific_secondary: run: |- @@ -13234,7 +12673,7 @@ actions: highly_sensitive: dataset: output/data/input_adults_2017_2018_specific_secondary.arrow - process_dataset_adults_s2_specific_secondary: + process_cohort_adults_s2_specific_secondary: run: r:latest analysis/data_processing.R adults season2_start_date season2_end_date specific secondary adults s2 2017_2018 specific secondary season2_start_date season2_end_date @@ -13245,164 +12684,46 @@ actions: highly_sensitive: cohort: output/data/input_processed_adults_2017_2018_specific_secondary.arrow - describe_dataset_adults_s2_specific_secondary: - run: r:latest analysis/report.R adults season2_start_date season2_end_date specific - secondary adults s2 2017_2018 specific secondary season2_start_date season2_end_date - needs: - - process_dataset_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_adults_2017_2018_specific_secondary.csv - - analyse_dataset_adults_rsv_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R adults season2_start_date season2_end_date + describe_cohort_adults_s2: + run: r:latest analysis/cohort_description.R adults season2_start_date season2_end_date specific secondary adults s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - - process_dataset_adults_s2_specific_secondary + - process_cohort_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_adults_2017_2018_specific_*.csv + csv: output/table1/table1_adults_2017_2018.csv - analyse_dataset_adults_rsv_further_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season2_start_date - season2_end_date specific secondary adults s2 2017_2018 specific secondary season2_start_date - season2_end_date - needs: - - process_dataset_adults_s2_specific_secondary + generate_dataset_adults_s3_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2018_2019_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2018_2019.arrow + -- adults season3_start_date season3_end_date specific secondary adults s3 2018_2019 specific secondary season3_start_date season3_end_date outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_adults_2017_2018_specific_*.csv + highly_sensitive: + dataset: output/data/input_adults_2018_2019_specific_secondary.arrow - analyse_dataset_adults_flu_s2_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R adults season2_start_date season2_end_date - specific secondary adults s2 2017_2018 specific secondary season2_start_date - season2_end_date + process_cohort_adults_s3_specific_secondary: + run: r:latest analysis/data_processing.R adults season3_start_date season3_end_date + specific secondary adults s3 2018_2019 specific secondary season3_start_date + season3_end_date needs: - - process_dataset_adults_s2_specific_secondary + - generate_dataset_adults_s3_specific_secondary + - process_household_information_s3 outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_adults_2017_2018_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_adults_2018_2019_specific_secondary.arrow - analyse_dataset_adults_flu_further_s2_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R adults season2_start_date - season2_end_date specific secondary adults s2 2017_2018 specific secondary season2_start_date - season2_end_date - needs: - - process_dataset_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_adults_2017_2018_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - adults season2_start_date season2_end_date specific secondary adults s2 2017_2018 - specific secondary season2_start_date season2_end_date - needs: - - process_dataset_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_adults_2017_2018_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_further_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - adults season2_start_date season2_end_date specific secondary adults s2 2017_2018 - specific secondary season2_start_date season2_end_date - needs: - - process_dataset_adults_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2017_2018_specific_*.csv - - generate_dataset_adults_s3_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_adults_2018_2019_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_adults_2018_2019.arrow - -- adults season3_start_date season3_end_date specific secondary adults s3 2018_2019 specific secondary season3_start_date season3_end_date - outputs: - highly_sensitive: - dataset: output/data/input_adults_2018_2019_specific_secondary.arrow - - process_dataset_adults_s3_specific_secondary: - run: r:latest analysis/data_processing.R adults season3_start_date season3_end_date - specific secondary adults s3 2018_2019 specific secondary season3_start_date - season3_end_date - needs: - - generate_dataset_adults_s3_specific_secondary - - process_household_information_s3 - outputs: - highly_sensitive: - cohort: output/data/input_processed_adults_2018_2019_specific_secondary.arrow - - describe_dataset_adults_s3_specific_secondary: - run: r:latest analysis/report.R adults season3_start_date season3_end_date specific - secondary adults s3 2018_2019 specific secondary season3_start_date season3_end_date - needs: - - process_dataset_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_adults_2018_2019_specific_secondary.csv - - analyse_dataset_adults_rsv_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R adults season3_start_date season3_end_date - specific secondary adults s3 2018_2019 specific secondary season3_start_date - season3_end_date - needs: - - process_dataset_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_adults_2018_2019_specific_*.csv - - analyse_dataset_adults_rsv_further_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season3_start_date - season3_end_date specific secondary adults s3 2018_2019 specific secondary season3_start_date - season3_end_date - needs: - - process_dataset_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_adults_2018_2019_specific_*.csv - - analyse_dataset_adults_flu_s3_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R adults season3_start_date season3_end_date + describe_cohort_adults_s3: + run: r:latest analysis/cohort_description.R adults season3_start_date season3_end_date specific secondary adults s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_adults_2018_2019_specific_*.csv - - analyse_dataset_adults_flu_further_s3_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R adults season3_start_date - season3_end_date specific secondary adults s3 2018_2019 specific secondary season3_start_date - season3_end_date - needs: - - process_dataset_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_adults_2018_2019_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - adults season3_start_date season3_end_date specific secondary adults s3 2018_2019 - specific secondary season3_start_date season3_end_date - needs: - - process_dataset_adults_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_adults_2018_2019_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_further_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - adults season3_start_date season3_end_date specific secondary adults s3 2018_2019 - specific secondary season3_start_date season3_end_date - needs: - - process_dataset_adults_s3_specific_secondary + - process_cohort_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2018_2019_specific_*.csv + csv: output/table1/table1_adults_2018_2019.csv generate_dataset_adults_s4_specific_secondary: run: |- @@ -13414,7 +12735,7 @@ actions: highly_sensitive: dataset: output/data/input_adults_2019_2020_specific_secondary.arrow - process_dataset_adults_s4_specific_secondary: + process_cohort_adults_s4_specific_secondary: run: r:latest analysis/data_processing.R adults season4_start_date season4_end_date specific secondary adults s4 2019_2020 specific secondary season4_start_date season4_end_date @@ -13425,94 +12746,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_adults_2019_2020_specific_secondary.arrow - describe_dataset_adults_s4_specific_secondary: - run: r:latest analysis/report.R adults season4_start_date season4_end_date specific - secondary adults s4 2019_2020 specific secondary season4_start_date season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_adults_2019_2020_specific_secondary.csv - - analyse_dataset_adults_rsv_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R adults season4_start_date season4_end_date - specific secondary adults s4 2019_2020 specific secondary season4_start_date - season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_adults_2019_2020_specific_*.csv - - analyse_dataset_adults_rsv_further_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season4_start_date - season4_end_date specific secondary adults s4 2019_2020 specific secondary season4_start_date - season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_adults_2019_2020_specific_*.csv - - analyse_dataset_adults_flu_s4_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R adults season4_start_date season4_end_date + describe_cohort_adults_s4: + run: r:latest analysis/cohort_description.R adults season4_start_date season4_end_date specific secondary adults s4 2019_2020 specific secondary season4_start_date season4_end_date needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_adults_2019_2020_specific_*.csv - - analyse_dataset_adults_flu_further_s4_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R adults season4_start_date - season4_end_date specific secondary adults s4 2019_2020 specific secondary season4_start_date - season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_adults_2019_2020_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_s4_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - adults season4_start_date season4_end_date specific secondary adults s4 2019_2020 - specific secondary season4_start_date season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_adults_2019_2020_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_further_s4_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - adults season4_start_date season4_end_date specific secondary adults s4 2019_2020 - specific secondary season4_start_date season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2019_2020_specific_*.csv - - analyse_dataset_adults_covid_s4_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R adults season4_start_date - season4_end_date specific secondary adults s4 2019_2020 specific secondary season4_start_date - season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary + - process_cohort_adults_s4_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_adults_2019_2020_specific_secondary.csv - - analyse_dataset_adults_covid_further_s4_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R adults season4_start_date - season4_end_date specific secondary adults s4 2019_2020 specific secondary season4_start_date - season4_end_date - needs: - - process_dataset_adults_s4_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_adults_2019_2020_specific_secondary.csv + csv: output/table1/table1_adults_2019_2020.csv generate_dataset_adults_s5_specific_secondary: run: |- @@ -13524,7 +12766,7 @@ actions: highly_sensitive: dataset: output/data/input_adults_2020_2021_specific_secondary.arrow - process_dataset_adults_s5_specific_secondary: + process_cohort_adults_s5_specific_secondary: run: r:latest analysis/data_processing.R adults season5_start_date season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date season5_end_date @@ -13535,94 +12777,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_adults_2020_2021_specific_secondary.arrow - describe_dataset_adults_s5_specific_secondary: - run: r:latest analysis/report.R adults season5_start_date season5_end_date specific - secondary adults s5 2020_2021 specific secondary season5_start_date season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_adults_2020_2021_specific_secondary.csv - - analyse_dataset_adults_rsv_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R adults season5_start_date season5_end_date - specific secondary adults s5 2020_2021 specific secondary season5_start_date - season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_adults_2020_2021_specific_*.csv - - analyse_dataset_adults_rsv_further_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season5_start_date - season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date - season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_adults_2020_2021_specific_*.csv - - analyse_dataset_adults_flu_s5_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R adults season5_start_date season5_end_date + describe_cohort_adults_s5: + run: r:latest analysis/cohort_description.R adults season5_start_date season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_adults_2020_2021_specific_*.csv - - analyse_dataset_adults_flu_further_s5_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R adults season5_start_date - season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date - season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_adults_2020_2021_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - adults season5_start_date season5_end_date specific secondary adults s5 2020_2021 - specific secondary season5_start_date season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_adults_2020_2021_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_further_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - adults season5_start_date season5_end_date specific secondary adults s5 2020_2021 - specific secondary season5_start_date season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2020_2021_specific_*.csv - - analyse_dataset_adults_covid_s5_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R adults season5_start_date - season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date - season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_adults_2020_2021_specific_secondary.csv - - analyse_dataset_adults_covid_further_s5_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R adults season5_start_date - season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date - season5_end_date - needs: - - process_dataset_adults_s5_specific_secondary + - process_cohort_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_adults_2020_2021_specific_secondary.csv + csv: output/table1/table1_adults_2020_2021.csv generate_dataset_adults_s6_specific_secondary: run: |- @@ -13634,7 +12797,7 @@ actions: highly_sensitive: dataset: output/data/input_adults_2021_2022_specific_secondary.arrow - process_dataset_adults_s6_specific_secondary: + process_cohort_adults_s6_specific_secondary: run: r:latest analysis/data_processing.R adults season6_start_date season6_end_date specific secondary adults s6 2021_2022 specific secondary season6_start_date season6_end_date @@ -13645,106 +12808,27 @@ actions: highly_sensitive: cohort: output/data/input_processed_adults_2021_2022_specific_secondary.arrow - describe_dataset_adults_s6_specific_secondary: - run: r:latest analysis/report.R adults season6_start_date season6_end_date specific - secondary adults s6 2021_2022 specific secondary season6_start_date season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_adults_2021_2022_specific_secondary.csv - - analyse_dataset_adults_rsv_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R adults season6_start_date season6_end_date + describe_cohort_adults_s6: + run: r:latest analysis/cohort_description.R adults season6_start_date season6_end_date specific secondary adults s6 2021_2022 specific secondary season6_start_date season6_end_date needs: - - process_dataset_adults_s6_specific_secondary + - process_cohort_adults_s6_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_adults_2021_2022_specific_*.csv + csv: output/table1/table1_adults_2021_2022.csv - analyse_dataset_adults_rsv_further_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season6_start_date - season6_end_date specific secondary adults s6 2021_2022 specific secondary season6_start_date - season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary + generate_dataset_adults_s7_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_adults_2022_2023_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow + -- adults season7_start_date season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date season7_end_date outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_adults_2021_2022_specific_*.csv + highly_sensitive: + dataset: output/data/input_adults_2022_2023_specific_secondary.arrow - analyse_dataset_adults_flu_s6_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R adults season6_start_date season6_end_date - specific secondary adults s6 2021_2022 specific secondary season6_start_date - season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_adults_2021_2022_specific_*.csv - - analyse_dataset_adults_flu_further_s6_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R adults season6_start_date - season6_end_date specific secondary adults s6 2021_2022 specific secondary season6_start_date - season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_adults_2021_2022_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - adults season6_start_date season6_end_date specific secondary adults s6 2021_2022 - specific secondary season6_start_date season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_adults_2021_2022_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_further_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - adults season6_start_date season6_end_date specific secondary adults s6 2021_2022 - specific secondary season6_start_date season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2021_2022_specific_*.csv - - analyse_dataset_adults_covid_s6_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R adults season6_start_date - season6_end_date specific secondary adults s6 2021_2022 specific secondary season6_start_date - season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_adults_2021_2022_specific_secondary.csv - - analyse_dataset_adults_covid_further_s6_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R adults season6_start_date - season6_end_date specific secondary adults s6 2021_2022 specific secondary season6_start_date - season6_end_date - needs: - - process_dataset_adults_s6_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_adults_2021_2022_specific_secondary.csv - - generate_dataset_adults_s7_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_adults_2022_2023_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_adults_2022_2023.arrow - -- adults season7_start_date season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date season7_end_date - outputs: - highly_sensitive: - dataset: output/data/input_adults_2022_2023_specific_secondary.arrow - - process_dataset_adults_s7_specific_secondary: + process_cohort_adults_s7_specific_secondary: run: r:latest analysis/data_processing.R adults season7_start_date season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date season7_end_date @@ -13755,98 +12839,18 @@ actions: highly_sensitive: cohort: output/data/input_processed_adults_2022_2023_specific_secondary.arrow - describe_dataset_adults_s7_specific_secondary: - run: r:latest analysis/report.R adults season7_start_date season7_end_date specific - secondary adults s7 2022_2023 specific secondary season7_start_date season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_adults_2022_2023_specific_secondary.csv - - analyse_dataset_adults_rsv_s7_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R adults season7_start_date season7_end_date - specific secondary adults s7 2022_2023 specific secondary season7_start_date - season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_adults_2022_2023_specific_*.csv - - analyse_dataset_adults_rsv_further_s7_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season7_start_date - season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date - season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_adults_2022_2023_specific_*.csv - - analyse_dataset_adults_flu_s7_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R adults season7_start_date season7_end_date + describe_cohort_adults_s7: + run: r:latest analysis/cohort_description.R adults season7_start_date season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date season7_end_date needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_adults_2022_2023_specific_*.csv - - analyse_dataset_adults_flu_further_s7_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R adults season7_start_date - season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date - season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_adults_2022_2023_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - adults season7_start_date season7_end_date specific secondary adults s7 2022_2023 - specific secondary season7_start_date season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_adults_2022_2023_specific_*.csv - - analyse_dataset_adults_overall_and_all_cause_further_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - adults season7_start_date season7_end_date specific secondary adults s7 2022_2023 - specific secondary season7_start_date season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2022_2023_specific_*.csv - - analyse_dataset_adults_covid_s7_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R adults season7_start_date - season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date - season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary + - process_cohort_adults_s7_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_adults_2022_2023_specific_secondary.csv - - analyse_dataset_adults_covid_further_s7_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R adults season7_start_date - season7_end_date specific secondary adults s7 2022_2023 specific secondary season7_start_date - season7_end_date - needs: - - process_dataset_adults_s7_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_adults_2022_2023_specific_secondary.csv + csv: output/table1/table1_adults_2022_2023.csv ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Children and Adolescents, Codelist Type: Specific, Investigation - Type: Secondary + ## Cohort: Children and Adolescents ## # # # # # # # # # # # # # # # # # # # generate_dataset_children_and_adolescents_s1_specific_secondary: @@ -13859,7 +12863,7 @@ actions: highly_sensitive: dataset: output/data/input_children_and_adolescents_2016_2017_specific_secondary.arrow - process_dataset_children_and_adolescents_s1_specific_secondary: + process_cohort_children_and_adolescents_s1_specific_secondary: run: r:latest analysis/data_processing.R children_and_adolescents season1_start_date season1_end_date specific secondary children_and_adolescents s1 2016_2017 specific secondary season1_start_date season1_end_date @@ -13870,77 +12874,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_children_and_adolescents_2016_2017_specific_secondary.arrow - describe_dataset_children_and_adolescents_s1_specific_secondary: - run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date - specific secondary children_and_adolescents s1 2016_2017 specific secondary - season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2016_2017_specific_secondary.csv - - analyse_dataset_children_and_adolescents_rsv_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season1_start_date - season1_end_date specific secondary children_and_adolescents s1 2016_2017 specific - secondary season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_children_and_adolescents_2016_2017_specific_*.csv - - analyse_dataset_children_and_adolescents_rsv_further_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season1_start_date season1_end_date specific secondary children_and_adolescents - s1 2016_2017 specific secondary season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2016_2017_specific_*.csv - - analyse_dataset_children_and_adolescents_flu_s1_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season1_start_date + describe_cohort_children_and_adolescents_s1: + run: r:latest analysis/cohort_description.R children_and_adolescents season1_start_date season1_end_date specific secondary children_and_adolescents s1 2016_2017 specific secondary season1_start_date season1_end_date needs: - - process_dataset_children_and_adolescents_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_children_and_adolescents_2016_2017_specific_*.csv - - analyse_dataset_children_and_adolescents_flu_further_s1_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents - season1_start_date season1_end_date specific secondary children_and_adolescents - s1 2016_2017 specific secondary season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2016_2017_specific_*.csv - - analyse_dataset_children_and_adolescents_overall_and_all_cause_s1_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - children_and_adolescents season1_start_date season1_end_date specific secondary - children_and_adolescents s1 2016_2017 specific secondary season1_start_date - season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2016_2017_specific_*.csv - - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s1_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - children_and_adolescents season1_start_date season1_end_date specific secondary - children_and_adolescents s1 2016_2017 specific secondary season1_start_date - season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_secondary + - process_cohort_children_and_adolescents_s1_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2016_2017_specific_*.csv + csv: output/table1/table1_children_and_adolescents_2016_2017.csv generate_dataset_children_and_adolescents_s2_specific_secondary: run: |- @@ -13952,7 +12894,7 @@ actions: highly_sensitive: dataset: output/data/input_children_and_adolescents_2017_2018_specific_secondary.arrow - process_dataset_children_and_adolescents_s2_specific_secondary: + process_cohort_children_and_adolescents_s2_specific_secondary: run: r:latest analysis/data_processing.R children_and_adolescents season2_start_date season2_end_date specific secondary children_and_adolescents s2 2017_2018 specific secondary season2_start_date season2_end_date @@ -13963,77 +12905,15 @@ actions: highly_sensitive: cohort: output/data/input_processed_children_and_adolescents_2017_2018_specific_secondary.arrow - describe_dataset_children_and_adolescents_s2_specific_secondary: - run: r:latest analysis/report.R children_and_adolescents season2_start_date season2_end_date - specific secondary children_and_adolescents s2 2017_2018 specific secondary - season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2017_2018_specific_secondary.csv - - analyse_dataset_children_and_adolescents_rsv_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season2_start_date - season2_end_date specific secondary children_and_adolescents s2 2017_2018 specific - secondary season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_children_and_adolescents_2017_2018_specific_*.csv - - analyse_dataset_children_and_adolescents_rsv_further_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season2_start_date season2_end_date specific secondary children_and_adolescents - s2 2017_2018 specific secondary season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2017_2018_specific_*.csv - - analyse_dataset_children_and_adolescents_flu_s2_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season2_start_date + describe_cohort_children_and_adolescents_s2: + run: r:latest analysis/cohort_description.R children_and_adolescents season2_start_date season2_end_date specific secondary children_and_adolescents s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_children_and_adolescents_2017_2018_specific_*.csv - - analyse_dataset_children_and_adolescents_flu_further_s2_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents - season2_start_date season2_end_date specific secondary children_and_adolescents - s2 2017_2018 specific secondary season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2017_2018_specific_*.csv - - analyse_dataset_children_and_adolescents_overall_and_all_cause_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - children_and_adolescents season2_start_date season2_end_date specific secondary - children_and_adolescents s2 2017_2018 specific secondary season2_start_date - season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2017_2018_specific_*.csv - - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - children_and_adolescents season2_start_date season2_end_date specific secondary - children_and_adolescents s2 2017_2018 specific secondary season2_start_date - season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_secondary + - process_cohort_children_and_adolescents_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2017_2018_specific_*.csv + csv: output/table1/table1_children_and_adolescents_2017_2018.csv generate_dataset_children_and_adolescents_s3_specific_secondary: run: |- @@ -14045,7 +12925,7 @@ actions: highly_sensitive: dataset: output/data/input_children_and_adolescents_2018_2019_specific_secondary.arrow - process_dataset_children_and_adolescents_s3_specific_secondary: + process_cohort_children_and_adolescents_s3_specific_secondary: run: r:latest analysis/data_processing.R children_and_adolescents season3_start_date season3_end_date specific secondary children_and_adolescents s3 2018_2019 specific secondary season3_start_date season3_end_date @@ -14056,1544 +12936,1836 @@ actions: highly_sensitive: cohort: output/data/input_processed_children_and_adolescents_2018_2019_specific_secondary.arrow - describe_dataset_children_and_adolescents_s3_specific_secondary: - run: r:latest analysis/report.R children_and_adolescents season3_start_date season3_end_date - specific secondary children_and_adolescents s3 2018_2019 specific secondary - season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2018_2019_specific_secondary.csv - - analyse_dataset_children_and_adolescents_rsv_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season3_start_date + describe_cohort_children_and_adolescents_s3: + run: r:latest analysis/cohort_description.R children_and_adolescents season3_start_date season3_end_date specific secondary children_and_adolescents s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s3_specific_secondary + - process_cohort_children_and_adolescents_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_children_and_adolescents_2018_2019_specific_*.csv + csv: output/table1/table1_children_and_adolescents_2018_2019.csv - analyse_dataset_children_and_adolescents_rsv_further_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season3_start_date season3_end_date specific secondary children_and_adolescents - s3 2018_2019 specific secondary season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_specific_secondary + generate_dataset_children_and_adolescents_s4_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2019_2020_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2019_2020.arrow + -- children_and_adolescents season4_start_date season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific secondary season4_start_date season4_end_date outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2018_2019_specific_*.csv + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2019_2020_specific_secondary.arrow - analyse_dataset_children_and_adolescents_flu_s3_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season3_start_date - season3_end_date specific secondary children_and_adolescents s3 2018_2019 specific - secondary season3_start_date season3_end_date + process_cohort_children_and_adolescents_s4_specific_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season4_start_date + season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific + secondary season4_start_date season4_end_date needs: - - process_dataset_children_and_adolescents_s3_specific_secondary + - generate_dataset_children_and_adolescents_s4_specific_secondary + - process_household_information_s4 outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_children_and_adolescents_2018_2019_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2019_2020_specific_secondary.arrow - analyse_dataset_children_and_adolescents_flu_further_s3_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents - season3_start_date season3_end_date specific secondary children_and_adolescents - s3 2018_2019 specific secondary season3_start_date season3_end_date + describe_cohort_children_and_adolescents_s4: + run: r:latest analysis/cohort_description.R children_and_adolescents season4_start_date + season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific + secondary season4_start_date season4_end_date needs: - - process_dataset_children_and_adolescents_s3_specific_secondary + - process_cohort_children_and_adolescents_s4_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2018_2019_specific_*.csv + csv: output/table1/table1_children_and_adolescents_2019_2020.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - children_and_adolescents season3_start_date season3_end_date specific secondary - children_and_adolescents s3 2018_2019 specific secondary season3_start_date - season3_end_date + generate_dataset_children_and_adolescents_s5_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2020_2021_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2020_2021.arrow + -- children_and_adolescents season5_start_date season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific secondary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2020_2021_specific_secondary.arrow + + process_cohort_children_and_adolescents_s5_specific_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season5_start_date + season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific + secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s3_specific_secondary + - generate_dataset_children_and_adolescents_s5_specific_secondary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2020_2021_specific_secondary.arrow + + describe_cohort_children_and_adolescents_s5: + run: r:latest analysis/cohort_description.R children_and_adolescents season5_start_date + season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific + secondary season5_start_date season5_end_date + needs: + - process_cohort_children_and_adolescents_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2018_2019_specific_*.csv + csv: output/table1/table1_children_and_adolescents_2020_2021.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - children_and_adolescents season3_start_date season3_end_date specific secondary - children_and_adolescents s3 2018_2019 specific secondary season3_start_date + generate_dataset_children_and_adolescents_s6_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2021_2022_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2021_2022.arrow + -- children_and_adolescents season6_start_date season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific secondary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2021_2022_specific_secondary.arrow + + process_cohort_children_and_adolescents_s6_specific_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season6_start_date + season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific + secondary season6_start_date season6_end_date + needs: + - generate_dataset_children_and_adolescents_s6_specific_secondary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2021_2022_specific_secondary.arrow + + describe_cohort_children_and_adolescents_s6: + run: r:latest analysis/cohort_description.R children_and_adolescents season6_start_date + season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific + secondary season6_start_date season6_end_date + needs: + - process_cohort_children_and_adolescents_s6_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_children_and_adolescents_2021_2022.csv + + generate_dataset_children_and_adolescents_s7_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_children_and_adolescents_2022_2023_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow + -- children_and_adolescents season7_start_date season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific secondary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_children_and_adolescents_2022_2023_specific_secondary.arrow + + process_cohort_children_and_adolescents_s7_specific_secondary: + run: r:latest analysis/data_processing.R children_and_adolescents season7_start_date + season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific + secondary season7_start_date season7_end_date + needs: + - generate_dataset_children_and_adolescents_s7_specific_secondary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_2022_2023_specific_secondary.arrow + + describe_cohort_children_and_adolescents_s7: + run: r:latest analysis/cohort_description.R children_and_adolescents season7_start_date + season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific + secondary season7_start_date season7_end_date + needs: + - process_cohort_children_and_adolescents_s7_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_children_and_adolescents_2022_2023.csv + + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Infants + ## # # # # # # # # # # # # # # # # # # # + + generate_dataset_infants_s1_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2016_2017_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow + -- infants season1_start_date season1_end_date specific secondary infants s1 2016_2017 specific secondary season1_start_date season1_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2016_2017_specific_secondary.arrow + + process_cohort_infants_s1_specific_secondary: + run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date + specific secondary infants s1 2016_2017 specific secondary season1_start_date + season1_end_date + needs: + - generate_dataset_infants_s1_specific_secondary + - process_household_information_s1 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2016_2017_specific_secondary.arrow + + describe_cohort_infants_s1: + run: r:latest analysis/cohort_description.R infants season1_start_date season1_end_date + specific secondary infants s1 2016_2017 specific secondary season1_start_date + season1_end_date + needs: + - process_cohort_infants_s1_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_infants_2016_2017.csv + + generate_dataset_infants_s2_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2017_2018_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow + -- infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 specific secondary season2_start_date season2_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2017_2018_specific_secondary.arrow + + process_cohort_infants_s2_specific_secondary: + run: r:latest analysis/data_processing.R infants season2_start_date season2_end_date + specific secondary infants s2 2017_2018 specific secondary season2_start_date + season2_end_date + needs: + - generate_dataset_infants_s2_specific_secondary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2017_2018_specific_secondary.arrow + + describe_cohort_infants_s2: + run: r:latest analysis/cohort_description.R infants season2_start_date season2_end_date + specific secondary infants s2 2017_2018 specific secondary season2_start_date + season2_end_date + needs: + - process_cohort_infants_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_infants_2017_2018.csv + + generate_dataset_infants_s3_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2018_2019_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow + -- infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 specific secondary season3_start_date season3_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2018_2019_specific_secondary.arrow + + process_cohort_infants_s3_specific_secondary: + run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date + specific secondary infants s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s3_specific_secondary + - generate_dataset_infants_s3_specific_secondary + - process_household_information_s3 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2018_2019_specific_secondary.arrow + + describe_cohort_infants_s3: + run: r:latest analysis/cohort_description.R infants season3_start_date season3_end_date + specific secondary infants s3 2018_2019 specific secondary season3_start_date + season3_end_date + needs: + - process_cohort_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2018_2019_specific_*.csv + csv: output/table1/table1_infants_2018_2019.csv - generate_dataset_children_and_adolescents_s4_specific_secondary: + generate_dataset_infants_s4_specific_secondary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2019_2020_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2019_2020.arrow - -- children_and_adolescents season4_start_date season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific secondary season4_start_date season4_end_date + --output output/data/input_infants_2019_2020_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow + -- infants season4_start_date season4_end_date specific secondary infants s4 2019_2020 specific secondary season4_start_date season4_end_date outputs: highly_sensitive: - dataset: output/data/input_children_and_adolescents_2019_2020_specific_secondary.arrow + dataset: output/data/input_infants_2019_2020_specific_secondary.arrow - process_dataset_children_and_adolescents_s4_specific_secondary: - run: r:latest analysis/data_processing.R children_and_adolescents season4_start_date - season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific - secondary season4_start_date season4_end_date + process_cohort_infants_s4_specific_secondary: + run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date + specific secondary infants s4 2019_2020 specific secondary season4_start_date + season4_end_date needs: - - generate_dataset_children_and_adolescents_s4_specific_secondary + - generate_dataset_infants_s4_specific_secondary - process_household_information_s4 outputs: highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2019_2020_specific_secondary.arrow + cohort: output/data/input_processed_infants_2019_2020_specific_secondary.arrow + + describe_cohort_infants_s4: + run: r:latest analysis/cohort_description.R infants season4_start_date season4_end_date + specific secondary infants s4 2019_2020 specific secondary season4_start_date + season4_end_date + needs: + - process_cohort_infants_s4_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_infants_2019_2020.csv + + generate_dataset_infants_s5_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2020_2021_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow + -- infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 specific secondary season5_start_date season5_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2020_2021_specific_secondary.arrow + + process_cohort_infants_s5_specific_secondary: + run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date + specific secondary infants s5 2020_2021 specific secondary season5_start_date + season5_end_date + needs: + - generate_dataset_infants_s5_specific_secondary + - process_household_information_s5 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2020_2021_specific_secondary.arrow + + describe_cohort_infants_s5: + run: r:latest analysis/cohort_description.R infants season5_start_date season5_end_date + specific secondary infants s5 2020_2021 specific secondary season5_start_date + season5_end_date + needs: + - process_cohort_infants_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_infants_2020_2021.csv + + generate_dataset_infants_s6_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2021_2022_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2021_2022.arrow + -- infants season6_start_date season6_end_date specific secondary infants s6 2021_2022 specific secondary season6_start_date season6_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2021_2022_specific_secondary.arrow + + process_cohort_infants_s6_specific_secondary: + run: r:latest analysis/data_processing.R infants season6_start_date season6_end_date + specific secondary infants s6 2021_2022 specific secondary season6_start_date + season6_end_date + needs: + - generate_dataset_infants_s6_specific_secondary + - process_household_information_s6 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2021_2022_specific_secondary.arrow + + describe_cohort_infants_s6: + run: r:latest analysis/cohort_description.R infants season6_start_date season6_end_date + specific secondary infants s6 2021_2022 specific secondary season6_start_date + season6_end_date + needs: + - process_cohort_infants_s6_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_infants_2021_2022.csv + + generate_dataset_infants_s7_specific_secondary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2022_2023_specific_secondary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow + -- infants season7_start_date season7_end_date specific secondary infants s7 2022_2023 specific secondary season7_start_date season7_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2022_2023_specific_secondary.arrow + + process_cohort_infants_s7_specific_secondary: + run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date + specific secondary infants s7 2022_2023 specific secondary season7_start_date + season7_end_date + needs: + - generate_dataset_infants_s7_specific_secondary + - process_household_information_s7 + outputs: + highly_sensitive: + cohort: output/data/input_processed_infants_2022_2023_specific_secondary.arrow + + describe_cohort_infants_s7: + run: r:latest analysis/cohort_description.R infants season7_start_date season7_end_date + specific secondary infants s7 2022_2023 specific secondary season7_start_date + season7_end_date + needs: + - process_cohort_infants_s7_specific_secondary + outputs: + moderately_sensitive: + csv: output/table1/table1_infants_2022_2023.csv + + ## # # # # # # # # # # # # # # # # # # # + ## SECONDARY ANALYSES + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults, Codelist Type: Specific, Investigation Type: Secondary + + + ## # # # # # # # # # # # # # # # # # # # + + process_dataset_older_adults_s2_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R older_adults season2_start_date + season2_end_date specific secondary older_adults s2 2017_2018 specific secondary + season2_start_date season2_end_date + needs: + - generate_dataset_older_adults_s2_specific_secondary + - process_household_information_s2 + outputs: + highly_sensitive: + cohort: output/data/input_processed_older_adults_s2_specific_secondary.arrow + + describe_dataset_older_adults_s2_specific_secondary: + run: r:latest analysis/report.R older_adults season2_start_date season2_end_date + specific secondary older_adults s2 2017_2018 specific secondary season2_start_date + season2_end_date + needs: + - process_dataset_older_adults_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_older_adults_s2_specific_secondary.csv + + analyse_dataset_older_adults_rsv_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_models.R older_adults season2_start_date + season2_end_date specific secondary older_adults s2 2017_2018 specific secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_secondary/*_older_adults_2017_2018_specific_*.csv + + analyse_dataset_older_adults_rsv_further_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season2_start_date + season2_end_date specific secondary older_adults s2 2017_2018 specific secondary + season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_secondary/further_*_older_adults_2017_2018_specific_*.csv + + analyse_dataset_older_adults_overall_and_all_cause_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + older_adults season2_start_date season2_end_date specific secondary older_adults + s2 2017_2018 specific secondary season2_start_date season2_end_date + needs: + - process_dataset_older_adults_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2017_2018_specific_*.csv - describe_dataset_children_and_adolescents_s4_specific_secondary: - run: r:latest analysis/report.R children_and_adolescents season4_start_date season4_end_date - specific secondary children_and_adolescents s4 2019_2020 specific secondary - season4_start_date season4_end_date + analyse_dataset_older_adults_overall_and_all_cause_further_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R + older_adults season2_start_date season2_end_date specific secondary older_adults + s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_older_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2019_2020_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season4_start_date - season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific - secondary season4_start_date season4_end_date + process_dataset_older_adults_s3_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R older_adults season3_start_date + season3_end_date specific secondary older_adults s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - generate_dataset_older_adults_s3_specific_secondary + - process_household_information_s3 outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_children_and_adolescents_2019_2020_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_older_adults_s3_specific_secondary.arrow - analyse_dataset_children_and_adolescents_rsv_further_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season4_start_date season4_end_date specific secondary children_and_adolescents - s4 2019_2020 specific secondary season4_start_date season4_end_date + describe_dataset_older_adults_s3_specific_secondary: + run: r:latest analysis/report.R older_adults season3_start_date season3_end_date + specific secondary older_adults s3 2018_2019 specific secondary season3_start_date + season3_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_older_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2019_2020_specific_*.csv + csv: output/results/rates/rates_older_adults_s3_specific_secondary.csv - analyse_dataset_children_and_adolescents_flu_s4_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season4_start_date - season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific - secondary season4_start_date season4_end_date + analyse_dataset_older_adults_flu_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_models.R older_adults season3_start_date + season3_end_date specific secondary older_adults s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_older_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_children_and_adolescents_2019_2020_specific_*.csv + csv: output/results/models/flu_secondary/*_older_adults_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_flu_further_s4_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents - season4_start_date season4_end_date specific secondary children_and_adolescents - s4 2019_2020 specific secondary season4_start_date season4_end_date + analyse_dataset_older_adults_flu_further_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_models.R older_adults season3_start_date + season3_end_date specific secondary older_adults s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_older_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2019_2020_specific_*.csv + csv: output/results/models/flu_secondary/further_*_older_adults_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_s4_specific_secondary: + analyse_dataset_older_adults_overall_and_all_cause_s3_specific_secondary: run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - children_and_adolescents season4_start_date season4_end_date specific secondary - children_and_adolescents s4 2019_2020 specific secondary season4_start_date - season4_end_date + older_adults season3_start_date season3_end_date specific secondary older_adults + s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_older_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2019_2020_specific_*.csv + csv: output/results/models/overall_and_all_cause_secondary/*_older_adults_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s4_specific_secondary: + analyse_dataset_older_adults_overall_and_all_cause_further_s3_specific_secondary: run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - children_and_adolescents season4_start_date season4_end_date specific secondary - children_and_adolescents s4 2019_2020 specific secondary season4_start_date - season4_end_date + older_adults season3_start_date season3_end_date specific secondary older_adults + s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_older_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2019_2020_specific_*.csv + csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_covid_s4_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R children_and_adolescents season4_start_date - season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific - secondary season4_start_date season4_end_date + process_dataset_older_adults_s5_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R older_adults season5_start_date + season5_end_date specific secondary older_adults s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - generate_dataset_older_adults_s5_specific_secondary + - process_household_information_s5 outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_children_and_adolescents_2019_2020_specific_secondary.csv + highly_sensitive: + cohort: output/data/input_processed_older_adults_s5_specific_secondary.arrow - analyse_dataset_children_and_adolescents_covid_further_s4_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R children_and_adolescents - season4_start_date season4_end_date specific secondary children_and_adolescents - s4 2019_2020 specific secondary season4_start_date season4_end_date + describe_dataset_older_adults_s5_specific_secondary: + run: r:latest analysis/report.R older_adults season5_start_date season5_end_date + specific secondary older_adults s5 2020_2021 specific secondary season5_start_date + season5_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_older_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_children_and_adolescents_2019_2020_specific_secondary.csv - - generate_dataset_children_and_adolescents_s5_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2020_2021_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2020_2021.arrow - -- children_and_adolescents season5_start_date season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific secondary season5_start_date season5_end_date - outputs: - highly_sensitive: - dataset: output/data/input_children_and_adolescents_2020_2021_specific_secondary.arrow + csv: output/results/rates/rates_older_adults_s5_specific_secondary.csv - process_dataset_children_and_adolescents_s5_specific_secondary: - run: r:latest analysis/data_processing.R children_and_adolescents season5_start_date - season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific - secondary season5_start_date season5_end_date + analyse_dataset_older_adults_covid_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_models.R older_adults season5_start_date + season5_end_date specific secondary older_adults s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - generate_dataset_children_and_adolescents_s5_specific_secondary - - process_household_information_s5 + - process_dataset_older_adults_s5_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2020_2021_specific_secondary.arrow + moderately_sensitive: + csv: output/results/models/covid_model_outputs_older_adults_2020_2021_specific_secondary.csv - describe_dataset_children_and_adolescents_s5_specific_secondary: - run: r:latest analysis/report.R children_and_adolescents season5_start_date season5_end_date - specific secondary children_and_adolescents s5 2020_2021 specific secondary + analyse_dataset_older_adults_covid_further_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_models.R older_adults season5_start_date + season5_end_date specific secondary older_adults s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_older_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2020_2021_specific_secondary.csv + csv: output/results/models/further_covid_model_outputs_older_adults_2020_2021_specific_secondary.csv - analyse_dataset_children_and_adolescents_rsv_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season5_start_date - season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific - secondary season5_start_date season5_end_date + analyse_dataset_older_adults_overall_and_all_cause_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + older_adults season5_start_date season5_end_date specific secondary older_adults + s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_older_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_children_and_adolescents_2020_2021_specific_*.csv + csv: output/results/models/overall_and_all_cause_model_outputs_older_adults_2020_2021_specific_secondary.csv - analyse_dataset_children_and_adolescents_rsv_further_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season5_start_date season5_end_date specific secondary children_and_adolescents + analyse_dataset_older_adults_overall_and_all_cause_further_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R + older_adults season5_start_date season5_end_date specific secondary older_adults s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_older_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2020_2021_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_model_outputs_older_adults_2020_2021_specific_secondary.csv - analyse_dataset_children_and_adolescents_flu_s5_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season5_start_date - season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific - secondary season5_start_date season5_end_date + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Adults, Codelist Type: Specific, Investigation Type: Secondary + ## # # # # # # # # # # # # # # # # # # # + + process_dataset_adults_s2_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R adults season2_start_date + season2_end_date specific secondary adults s2 2017_2018 specific secondary season2_start_date + season2_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - generate_dataset_adults_s2_specific_secondary + - process_household_information_s2 outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_children_and_adolescents_2020_2021_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_adults_s2_specific_secondary.arrow - analyse_dataset_children_and_adolescents_flu_further_s5_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents - season5_start_date season5_end_date specific secondary children_and_adolescents - s5 2020_2021 specific secondary season5_start_date season5_end_date + describe_dataset_adults_s2_specific_secondary: + run: r:latest analysis/report.R adults season2_start_date season2_end_date specific + secondary adults s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2020_2021_specific_*.csv + csv: output/results/rates/rates_adults_s2_specific_secondary.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - children_and_adolescents season5_start_date season5_end_date specific secondary - children_and_adolescents s5 2020_2021 specific secondary season5_start_date - season5_end_date + analyse_dataset_adults_rsv_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_models.R adults season2_start_date season2_end_date + specific secondary adults s2 2017_2018 specific secondary season2_start_date + season2_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2020_2021_specific_*.csv + csv: output/results/models/rsv_secondary/*_adults_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - children_and_adolescents season5_start_date season5_end_date specific secondary - children_and_adolescents s5 2020_2021 specific secondary season5_start_date - season5_end_date + analyse_dataset_adults_rsv_further_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season2_start_date + season2_end_date specific secondary adults s2 2017_2018 specific secondary season2_start_date + season2_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2020_2021_specific_*.csv + csv: output/results/models/rsv_secondary/further_*_adults_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_covid_s5_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R children_and_adolescents season5_start_date - season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific - secondary season5_start_date season5_end_date + analyse_dataset_adults_overall_and_all_cause_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + adults season2_start_date season2_end_date specific secondary adults s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_children_and_adolescents_2020_2021_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_secondary/*_adults_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_covid_further_s5_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R children_and_adolescents - season5_start_date season5_end_date specific secondary children_and_adolescents - s5 2020_2021 specific secondary season5_start_date season5_end_date + analyse_dataset_adults_overall_and_all_cause_further_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R + adults season2_start_date season2_end_date specific secondary adults s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_adults_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_children_and_adolescents_2020_2021_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2017_2018_specific_*.csv - generate_dataset_children_and_adolescents_s6_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2021_2022_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2021_2022.arrow - -- children_and_adolescents season6_start_date season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific secondary season6_start_date season6_end_date + process_dataset_adults_s3_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R adults season3_start_date + season3_end_date specific secondary adults s3 2018_2019 specific secondary season3_start_date + season3_end_date + needs: + - generate_dataset_adults_s3_specific_secondary + - process_household_information_s3 outputs: highly_sensitive: - dataset: output/data/input_children_and_adolescents_2021_2022_specific_secondary.arrow + cohort: output/data/input_processed_adults_s3_specific_secondary.arrow - process_dataset_children_and_adolescents_s6_specific_secondary: - run: r:latest analysis/data_processing.R children_and_adolescents season6_start_date - season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific - secondary season6_start_date season6_end_date + describe_dataset_adults_s3_specific_secondary: + run: r:latest analysis/report.R adults season3_start_date season3_end_date specific + secondary adults s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - generate_dataset_children_and_adolescents_s6_specific_secondary - - process_household_information_s6 + - process_dataset_adults_s3_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2021_2022_specific_secondary.arrow + moderately_sensitive: + csv: output/results/rates/rates_adults_s3_specific_secondary.csv - describe_dataset_children_and_adolescents_s6_specific_secondary: - run: r:latest analysis/report.R children_and_adolescents season6_start_date season6_end_date - specific secondary children_and_adolescents s6 2021_2022 specific secondary - season6_start_date season6_end_date + analyse_dataset_adults_flu_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_models.R adults season3_start_date season3_end_date + specific secondary adults s3 2018_2019 specific secondary season3_start_date + season3_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2021_2022_specific_secondary.csv + csv: output/results/models/flu_secondary/*_adults_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season6_start_date - season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific - secondary season6_start_date season6_end_date + analyse_dataset_adults_flu_further_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_models.R adults season3_start_date + season3_end_date specific secondary adults s3 2018_2019 specific secondary season3_start_date + season3_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_children_and_adolescents_2021_2022_specific_*.csv + csv: output/results/models/flu_secondary/further_*_adults_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season6_start_date season6_end_date specific secondary children_and_adolescents - s6 2021_2022 specific secondary season6_start_date season6_end_date + analyse_dataset_adults_overall_and_all_cause_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + adults season3_start_date season3_end_date specific secondary adults s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2021_2022_specific_*.csv + csv: output/results/models/overall_and_all_cause_secondary/*_adults_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s6_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season6_start_date - season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific - secondary season6_start_date season6_end_date + analyse_dataset_adults_overall_and_all_cause_further_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R + adults season3_start_date season3_end_date specific secondary adults s3 2018_2019 + specific secondary season3_start_date season3_end_date + needs: + - process_dataset_adults_s3_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_secondary/further_*_adults_2018_2019_specific_*.csv + + process_dataset_adults_s5_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R adults season5_start_date + season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date + season5_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - generate_dataset_adults_s5_specific_secondary + - process_household_information_s5 outputs: - moderately_sensitive: - csv: output/results/models/flu_secondary/*_children_and_adolescents_2021_2022_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_adults_s5_specific_secondary.arrow - analyse_dataset_children_and_adolescents_flu_further_s6_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents - season6_start_date season6_end_date specific secondary children_and_adolescents - s6 2021_2022 specific secondary season6_start_date season6_end_date + describe_dataset_adults_s5_specific_secondary: + run: r:latest analysis/report.R adults season5_start_date season5_end_date specific + secondary adults s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2021_2022_specific_*.csv + csv: output/results/rates/rates_adults_s5_specific_secondary.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - children_and_adolescents season6_start_date season6_end_date specific secondary - children_and_adolescents s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_adults_covid_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_models.R adults season5_start_date + season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date + season5_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2021_2022_specific_*.csv + csv: output/results/models/covid_model_outputs_adults_2020_2021_specific_secondary.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - children_and_adolescents season6_start_date season6_end_date specific secondary - children_and_adolescents s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_adults_covid_further_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_models.R adults season5_start_date + season5_end_date specific secondary adults s5 2020_2021 specific secondary season5_start_date + season5_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2021_2022_specific_*.csv + csv: output/results/models/further_covid_model_outputs_adults_2020_2021_specific_secondary.csv - analyse_dataset_children_and_adolescents_covid_s6_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R children_and_adolescents season6_start_date - season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific - secondary season6_start_date season6_end_date + analyse_dataset_adults_overall_and_all_cause_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + adults season5_start_date season5_end_date specific secondary adults s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_children_and_adolescents_2021_2022_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_model_outputs_adults_2020_2021_specific_secondary.csv - analyse_dataset_children_and_adolescents_covid_further_s6_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R children_and_adolescents - season6_start_date season6_end_date specific secondary children_and_adolescents - s6 2021_2022 specific secondary season6_start_date season6_end_date + analyse_dataset_adults_overall_and_all_cause_further_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R + adults season5_start_date season5_end_date specific secondary adults s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_adults_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_children_and_adolescents_2021_2022_specific_secondary.csv + csv: output/results/models/further_overall_and_all_cause_model_outputs_adults_2020_2021_specific_secondary.csv - generate_dataset_children_and_adolescents_s7_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_children_and_adolescents_2022_2023_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_children_and_adolescents_2022_2023.arrow - -- children_and_adolescents season7_start_date season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific secondary season7_start_date season7_end_date - outputs: - highly_sensitive: - dataset: output/data/input_children_and_adolescents_2022_2023_specific_secondary.arrow + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Children and Adolescents, Codelist Type: Specific, Investigation + Type: Secondary + ## # # # # # # # # # # # # # # # # # # # - process_dataset_children_and_adolescents_s7_specific_secondary: - run: r:latest analysis/data_processing.R children_and_adolescents season7_start_date - season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific - secondary season7_start_date season7_end_date + process_dataset_children_and_adolescents_s2_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R children_and_adolescents + season2_start_date season2_end_date specific secondary children_and_adolescents + s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - - generate_dataset_children_and_adolescents_s7_specific_secondary - - process_household_information_s7 + - generate_dataset_children_and_adolescents_s2_specific_secondary + - process_household_information_s2 outputs: highly_sensitive: - cohort: output/data/input_processed_children_and_adolescents_2022_2023_specific_secondary.arrow + cohort: output/data/input_processed_children_and_adolescents_s2_specific_secondary.arrow - describe_dataset_children_and_adolescents_s7_specific_secondary: - run: r:latest analysis/report.R children_and_adolescents season7_start_date season7_end_date - specific secondary children_and_adolescents s7 2022_2023 specific secondary - season7_start_date season7_end_date + describe_dataset_children_and_adolescents_s2_specific_secondary: + run: r:latest analysis/report.R children_and_adolescents season2_start_date season2_end_date + specific secondary children_and_adolescents s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_children_and_adolescents_2022_2023_specific_secondary.csv + csv: output/results/rates/rates_children_and_adolescents_s2_specific_secondary.csv - analyse_dataset_children_and_adolescents_rsv_s7_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season7_start_date - season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific - secondary season7_start_date season7_end_date + analyse_dataset_children_and_adolescents_rsv_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_models.R children_and_adolescents season2_start_date + season2_end_date specific secondary children_and_adolescents s2 2017_2018 specific + secondary season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_children_and_adolescents_2022_2023_specific_*.csv + csv: output/results/models/rsv_secondary/*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s7_specific_secondary: + analyse_dataset_children_and_adolescents_rsv_further_s2_specific_secondary: run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season7_start_date season7_end_date specific secondary children_and_adolescents - s7 2022_2023 specific secondary season7_start_date season7_end_date + season2_start_date season2_end_date specific secondary children_and_adolescents + s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2022_2023_specific_*.csv + csv: output/results/models/rsv_secondary/further_*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s7_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season7_start_date - season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific - secondary season7_start_date season7_end_date + analyse_dataset_children_and_adolescents_overall_and_all_cause_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + children_and_adolescents season2_start_date season2_end_date specific secondary + children_and_adolescents s2 2017_2018 specific secondary season2_start_date + season2_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_children_and_adolescents_2022_2023_specific_*.csv + csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_flu_further_s7_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents - season7_start_date season7_end_date specific secondary children_and_adolescents - s7 2022_2023 specific secondary season7_start_date season7_end_date + analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R + children_and_adolescents season2_start_date season2_end_date specific secondary + children_and_adolescents s2 2017_2018 specific secondary season2_start_date + season2_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2022_2023_specific_*.csv + csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - children_and_adolescents season7_start_date season7_end_date specific secondary - children_and_adolescents s7 2022_2023 specific secondary season7_start_date - season7_end_date + process_dataset_children_and_adolescents_s3_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R children_and_adolescents + season3_start_date season3_end_date specific secondary children_and_adolescents + s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - generate_dataset_children_and_adolescents_s3_specific_secondary + - process_household_information_s3 outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2022_2023_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_s3_specific_secondary.arrow - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - children_and_adolescents season7_start_date season7_end_date specific secondary - children_and_adolescents s7 2022_2023 specific secondary season7_start_date - season7_end_date + describe_dataset_children_and_adolescents_s3_specific_secondary: + run: r:latest analysis/report.R children_and_adolescents season3_start_date season3_end_date + specific secondary children_and_adolescents s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2022_2023_specific_*.csv + csv: output/results/rates/rates_children_and_adolescents_s3_specific_secondary.csv - analyse_dataset_children_and_adolescents_covid_s7_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R children_and_adolescents season7_start_date - season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific - secondary season7_start_date season7_end_date + analyse_dataset_children_and_adolescents_flu_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season3_start_date + season3_end_date specific secondary children_and_adolescents s3 2018_2019 specific + secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_children_and_adolescents_2022_2023_specific_secondary.csv + csv: output/results/models/flu_secondary/*_children_and_adolescents_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_covid_further_s7_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R children_and_adolescents - season7_start_date season7_end_date specific secondary children_and_adolescents - s7 2022_2023 specific secondary season7_start_date season7_end_date + analyse_dataset_children_and_adolescents_flu_further_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_models.R children_and_adolescents + season3_start_date season3_end_date specific secondary children_and_adolescents + s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_children_and_adolescents_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_children_and_adolescents_2022_2023_specific_secondary.csv - - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Infants, Codelist Type: Specific, Investigation Type: Secondary - - - ## # # # # # # # # # # # # # # # # # # # - - generate_dataset_infants_s1_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2016_2017_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2016_2017.arrow - -- infants season1_start_date season1_end_date specific secondary infants s1 2016_2017 specific secondary season1_start_date season1_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2016_2017_specific_secondary.arrow + csv: output/results/models/flu_secondary/further_*_children_and_adolescents_2018_2019_specific_*.csv - process_dataset_infants_s1_specific_secondary: - run: r:latest analysis/data_processing.R infants season1_start_date season1_end_date - specific secondary infants s1 2016_2017 specific secondary season1_start_date - season1_end_date + analyse_dataset_children_and_adolescents_overall_and_all_cause_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + children_and_adolescents season3_start_date season3_end_date specific secondary + children_and_adolescents s3 2018_2019 specific secondary season3_start_date + season3_end_date needs: - - generate_dataset_infants_s1_specific_secondary - - process_household_information_s1 + - process_dataset_children_and_adolescents_s3_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2016_2017_specific_secondary.arrow + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2018_2019_specific_*.csv - describe_dataset_infants_s1_specific_secondary: - run: r:latest analysis/report.R infants season1_start_date season1_end_date specific - secondary infants s1 2016_2017 specific secondary season1_start_date season1_end_date + analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R + children_and_adolescents season3_start_date season3_end_date specific secondary + children_and_adolescents s3 2018_2019 specific secondary season3_start_date + season3_end_date needs: - - process_dataset_infants_s1_specific_secondary + - process_dataset_children_and_adolescents_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2016_2017_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2018_2019_specific_*.csv - analyse_dataset_infants_rsv_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R infants season1_start_date season1_end_date - specific secondary infants s1 2016_2017 specific secondary season1_start_date - season1_end_date + process_dataset_children_and_adolescents_s5_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R children_and_adolescents + season5_start_date season5_end_date specific secondary children_and_adolescents + s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s1_specific_secondary + - generate_dataset_children_and_adolescents_s5_specific_secondary + - process_household_information_s5 outputs: - moderately_sensitive: - csv: output/results/models/rsv_secondary/*_infants_2016_2017_specific_*.csv + highly_sensitive: + cohort: output/data/input_processed_children_and_adolescents_s5_specific_secondary.arrow - analyse_dataset_infants_rsv_further_s1_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R infants season1_start_date - season1_end_date specific secondary infants s1 2016_2017 specific secondary - season1_start_date season1_end_date + describe_dataset_children_and_adolescents_s5_specific_secondary: + run: r:latest analysis/report.R children_and_adolescents season5_start_date season5_end_date + specific secondary children_and_adolescents s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_infants_s1_specific_secondary + - process_dataset_children_and_adolescents_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_infants_2016_2017_specific_*.csv + csv: output/results/rates/rates_children_and_adolescents_s5_specific_secondary.csv - analyse_dataset_infants_flu_s1_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R infants season1_start_date season1_end_date - specific secondary infants s1 2016_2017 specific secondary season1_start_date - season1_end_date + analyse_dataset_children_and_adolescents_covid_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_models.R children_and_adolescents season5_start_date + season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific + secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s1_specific_secondary + - process_dataset_children_and_adolescents_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_infants_2016_2017_specific_*.csv + csv: output/results/models/covid_model_outputs_children_and_adolescents_2020_2021_specific_secondary.csv - analyse_dataset_infants_flu_further_s1_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R infants season1_start_date - season1_end_date specific secondary infants s1 2016_2017 specific secondary - season1_start_date season1_end_date + analyse_dataset_children_and_adolescents_covid_further_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_models.R children_and_adolescents + season5_start_date season5_end_date specific secondary children_and_adolescents + s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s1_specific_secondary + - process_dataset_children_and_adolescents_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_infants_2016_2017_specific_*.csv + csv: output/results/models/further_covid_model_outputs_children_and_adolescents_2020_2021_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_s1_specific_secondary: + analyse_dataset_children_and_adolescents_overall_and_all_cause_s5_specific_secondary: run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - infants season1_start_date season1_end_date specific secondary infants s1 2016_2017 - specific secondary season1_start_date season1_end_date + children_and_adolescents season5_start_date season5_end_date specific secondary + children_and_adolescents s5 2020_2021 specific secondary season5_start_date + season5_end_date needs: - - process_dataset_infants_s1_specific_secondary + - process_dataset_children_and_adolescents_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_infants_2016_2017_specific_*.csv + csv: output/results/models/overall_and_all_cause_model_outputs_children_and_adolescents_2020_2021_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_further_s1_specific_secondary: + analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s5_specific_secondary: run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - infants season1_start_date season1_end_date specific secondary infants s1 2016_2017 - specific secondary season1_start_date season1_end_date + children_and_adolescents season5_start_date season5_end_date specific secondary + children_and_adolescents s5 2020_2021 specific secondary season5_start_date + season5_end_date needs: - - process_dataset_infants_s1_specific_secondary + - process_dataset_children_and_adolescents_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_infants_2016_2017_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_model_outputs_children_and_adolescents_2020_2021_specific_secondary.csv - generate_dataset_infants_s2_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2017_2018_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow - -- infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 specific secondary season2_start_date season2_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2017_2018_specific_secondary.arrow + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Infants, Codelist Type: Specific, Investigation Type: Secondary + + + ## # # # # # # # # # # # # # # # # # # # process_dataset_infants_s2_specific_secondary: - run: r:latest analysis/data_processing.R infants season2_start_date season2_end_date - specific secondary infants s2 2017_2018 specific secondary season2_start_date - season2_end_date + run: r:latest analysis/secondary_analyses/data_processing_sec.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - generate_dataset_infants_s2_specific_secondary - process_household_information_s2 outputs: highly_sensitive: - cohort: output/data/input_processed_infants_2017_2018_specific_secondary.arrow + cohort: output/data/input_processed_infants_s2_specific_secondary.arrow + + describe_dataset_infants_s2_specific_secondary: + run: r:latest analysis/report.R infants season2_start_date season2_end_date specific + secondary infants s2 2017_2018 specific secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/rates/rates_infants_s2_specific_secondary.csv + + analyse_dataset_infants_rsv_ethnicity_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2017_2018_specific_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_specific_secondary.csv - describe_dataset_infants_s2_specific_secondary: - run: r:latest analysis/report.R infants season2_start_date season2_end_date specific - secondary infants s2 2017_2018 specific secondary season2_start_date season2_end_date + analyse_dataset_infants_rsv_ses_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2017_2018_specific_secondary.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_rsv_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R infants season2_start_date season2_end_date - specific secondary infants s2 2017_2018 specific secondary season2_start_date - season2_end_date + analyse_dataset_infants_overall_and_all_cause_ses_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_infants_2017_2018_specific_*.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_rsv_further_s2_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R infants season2_start_date + analyse_dataset_infants_rsv_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_infants_2017_2018_specific_*.csv + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_flu_s2_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R infants season2_start_date season2_end_date - specific secondary infants s2 2017_2018 specific secondary season2_start_date - season2_end_date + analyse_dataset_infants_overall_and_all_cause_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_infants_2017_2018_specific_*.csv + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_flu_further_s2_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R infants season2_start_date + analyse_dataset_infants_rsv_ethnicity_ses_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_infants_2017_2018_specific_*.csv + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 specific secondary season2_start_date season2_end_date needs: - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_infants_2017_2018_specific_*.csv + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_further_s2_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 - specific secondary season2_start_date season2_end_date + analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_hh_comp_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_infants_2017_2018_specific_*.csv - - generate_dataset_infants_s3_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2018_2019_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow - -- infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 specific secondary season3_start_date season3_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2018_2019_specific_secondary.arrow + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - process_dataset_infants_s3_specific_secondary: - run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date - specific secondary infants s3 2018_2019 specific secondary season3_start_date - season3_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - generate_dataset_infants_s3_specific_secondary - - process_household_information_s3 + - process_dataset_infants_s2_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2018_2019_specific_secondary.arrow + moderately_sensitive: + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - describe_dataset_infants_s3_specific_secondary: - run: r:latest analysis/report.R infants season3_start_date season3_end_date specific - secondary infants s3 2018_2019 specific secondary season3_start_date season3_end_date + analyse_dataset_infants_rsv_ses_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2018_2019_specific_secondary.csv + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_rsv_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R infants season3_start_date season3_end_date - specific secondary infants s3 2018_2019 specific secondary season3_start_date - season3_end_date + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_infants_2018_2019_specific_*.csv + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_rsv_further_s3_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R infants season3_start_date - season3_end_date specific secondary infants s3 2018_2019 specific secondary - season3_start_date season3_end_date + analyse_dataset_infants_rsv_full_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_infants_2018_2019_specific_*.csv + csv: output/results/models/rsv_full_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_flu_s3_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R infants season3_start_date season3_end_date - specific secondary infants s3 2018_2019 specific secondary season3_start_date - season3_end_date + analyse_dataset_infants_overall_and_all_cause_full_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_infants_2018_2019_specific_*.csv + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_flu_further_s3_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R infants season3_start_date - season3_end_date specific secondary infants s3 2018_2019 specific secondary - season3_start_date season3_end_date + analyse_dataset_infants_further_rsv_ethnicity_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_infants_2018_2019_specific_*.csv + csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 - specific secondary season3_start_date season3_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_infants_2018_2019_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_further_s3_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 - specific secondary season3_start_date season3_end_date + analyse_dataset_infants_further_rsv_ses_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_infants_2018_2019_specific_*.csv + csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_specific_secondary.csv - generate_dataset_infants_s4_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2019_2020_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow - -- infants season4_start_date season4_end_date specific secondary infants s4 2019_2020 specific secondary season4_start_date season4_end_date + analyse_dataset_infants_further_overall_and_all_cause_ses_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date + needs: + - process_dataset_infants_s2_specific_secondary outputs: - highly_sensitive: - dataset: output/data/input_infants_2019_2020_specific_secondary.arrow + moderately_sensitive: + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_specific_secondary.csv - process_dataset_infants_s4_specific_secondary: - run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date - specific secondary infants s4 2019_2020 specific secondary season4_start_date - season4_end_date + analyse_dataset_infants_further_rsv_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - generate_dataset_infants_s4_specific_secondary - - process_household_information_s4 + - process_dataset_infants_s2_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2019_2020_specific_secondary.arrow + moderately_sensitive: + csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - describe_dataset_infants_s4_specific_secondary: - run: r:latest analysis/report.R infants season4_start_date season4_end_date specific - secondary infants s4 2019_2020 specific secondary season4_start_date season4_end_date + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2019_2020_specific_secondary.csv + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_rsv_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R infants season4_start_date season4_end_date - specific secondary infants s4 2019_2020 specific secondary season4_start_date - season4_end_date + analyse_dataset_infants_further_rsv_ethnicity_ses_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants + season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_infants_2019_2020_specific_*.csv + csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_rsv_further_s4_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R infants season4_start_date - season4_end_date specific secondary infants s4 2019_2020 specific secondary - season4_start_date season4_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_infants_2019_2020_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_flu_s4_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R infants season4_start_date season4_end_date - specific secondary infants s4 2019_2020 specific secondary season4_start_date - season4_end_date + analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants + season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_infants_2019_2020_specific_*.csv + csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_flu_further_s4_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R infants season4_start_date - season4_end_date specific secondary infants s4 2019_2020 specific secondary - season4_start_date season4_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_infants_2019_2020_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_s4_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - infants season4_start_date season4_end_date specific secondary infants s4 2019_2020 - specific secondary season4_start_date season4_end_date + analyse_dataset_infants_further_rsv_ses_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_infants_2019_2020_specific_*.csv + csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_further_s4_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - infants season4_start_date season4_end_date specific secondary infants s4 2019_2020 - specific secondary season4_start_date season4_end_date + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_infants_2019_2020_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_covid_s4_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R infants season4_start_date - season4_end_date specific secondary infants s4 2019_2020 specific secondary - season4_start_date season4_end_date + analyse_dataset_infants_further_rsv_full_s2_specific_secondary: + run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season2_start_date + season2_end_date specific secondary infants s2 2017_2018 specific secondary + season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_infants_2019_2020_specific_secondary.csv + csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_specific_secondary.csv - analyse_dataset_infants_covid_further_s4_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R infants season4_start_date - season4_end_date specific secondary infants s4 2019_2020 specific secondary - season4_start_date season4_end_date + analyse_dataset_infants_further_overall_and_all_cause_full_s2_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R + infants season2_start_date season2_end_date specific secondary infants s2 2017_2018 + specific secondary season2_start_date season2_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s2_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_infants_2019_2020_specific_secondary.csv + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_secondary.csv - generate_dataset_infants_s5_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2020_2021_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow - -- infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 specific secondary season5_start_date season5_end_date + process_dataset_infants_s3_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date + needs: + - generate_dataset_infants_s3_specific_secondary + - process_household_information_s3 outputs: highly_sensitive: - dataset: output/data/input_infants_2020_2021_specific_secondary.arrow + cohort: output/data/input_processed_infants_s3_specific_secondary.arrow - process_dataset_infants_s5_specific_secondary: - run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date - specific secondary infants s5 2020_2021 specific secondary season5_start_date - season5_end_date + describe_dataset_infants_s3_specific_secondary: + run: r:latest analysis/report.R infants season3_start_date season3_end_date specific + secondary infants s3 2018_2019 specific secondary season3_start_date season3_end_date needs: - - generate_dataset_infants_s5_specific_secondary - - process_household_information_s5 + - process_dataset_infants_s3_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2020_2021_specific_secondary.arrow + moderately_sensitive: + csv: output/results/rates/rates_infants_s3_specific_secondary.csv - describe_dataset_infants_s5_specific_secondary: - run: r:latest analysis/report.R infants season5_start_date season5_end_date specific - secondary infants s5 2020_2021 specific secondary season5_start_date season5_end_date + analyse_dataset_infants_flu_ethnicity_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2020_2021_specific_secondary.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_rsv_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R infants season5_start_date season5_end_date - specific secondary infants s5 2020_2021 specific secondary season5_start_date - season5_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_infants_2020_2021_specific_*.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_rsv_further_s5_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R infants season5_start_date - season5_end_date specific secondary infants s5 2020_2021 specific secondary - season5_start_date season5_end_date + analyse_dataset_infants_flu_ses_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_infants_2020_2021_specific_*.csv + csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_flu_s5_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R infants season5_start_date season5_end_date - specific secondary infants s5 2020_2021 specific secondary season5_start_date - season5_end_date + analyse_dataset_infants_overall_and_all_cause_ses_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_infants_2020_2021_specific_*.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_flu_further_s5_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R infants season5_start_date - season5_end_date specific secondary infants s5 2020_2021 specific secondary - season5_start_date season5_end_date + analyse_dataset_infants_flu_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_infants_2020_2021_specific_*.csv + csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 - specific secondary season5_start_date season5_end_date + analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_infants_2020_2021_specific_*.csv + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_further_s5_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 - specific secondary season5_start_date season5_end_date + analyse_dataset_infants_flu_ethnicity_ses_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date + needs: + - process_dataset_infants_s3_specific_secondary + outputs: + moderately_sensitive: + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_secondary.csv + + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_infants_2020_2021_specific_*.csv + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_covid_s5_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R infants season5_start_date - season5_end_date specific secondary infants s5 2020_2021 specific secondary - season5_start_date season5_end_date + analyse_dataset_infants_flu_ethnicity_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_infants_2020_2021_specific_secondary.csv + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_covid_further_s5_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R infants season5_start_date - season5_end_date specific secondary infants s5 2020_2021 specific secondary - season5_start_date season5_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s5_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_infants_2020_2021_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - generate_dataset_infants_s6_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2021_2022_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2021_2022.arrow - -- infants season6_start_date season6_end_date specific secondary infants s6 2021_2022 specific secondary season6_start_date season6_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2021_2022_specific_secondary.arrow - - process_dataset_infants_s6_specific_secondary: - run: r:latest analysis/data_processing.R infants season6_start_date season6_end_date - specific secondary infants s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_infants_flu_ses_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - generate_dataset_infants_s6_specific_secondary - - process_household_information_s6 + - process_dataset_infants_s3_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2021_2022_specific_secondary.arrow + moderately_sensitive: + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - describe_dataset_infants_s6_specific_secondary: - run: r:latest analysis/report.R infants season6_start_date season6_end_date specific - secondary infants s6 2021_2022 specific secondary season6_start_date season6_end_date + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2021_2022_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_rsv_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R infants season6_start_date season6_end_date - specific secondary infants s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_infants_flu_full_s3_specific_secondary: + run: r:latest analysis/outcome_flu/flu_full_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_infants_2021_2022_specific_*.csv + csv: output/results/models/flu_full_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_rsv_further_s6_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R infants season6_start_date - season6_end_date specific secondary infants s6 2021_2022 specific secondary - season6_start_date season6_end_date + analyse_dataset_infants_overall_and_all_cause_full_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_infants_2021_2022_specific_*.csv + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_flu_s6_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R infants season6_start_date season6_end_date - specific secondary infants s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_infants_further_flu_ethnicity_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_infants_2021_2022_specific_*.csv + csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_flu_further_s6_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R infants season6_start_date - season6_end_date specific secondary infants s6 2021_2022 specific secondary - season6_start_date season6_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_infants_2021_2022_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - infants season6_start_date season6_end_date specific secondary infants s6 2021_2022 - specific secondary season6_start_date season6_end_date + analyse_dataset_infants_further_flu_ses_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_infants_2021_2022_specific_*.csv + csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_further_s6_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - infants season6_start_date season6_end_date specific secondary infants s6 2021_2022 - specific secondary season6_start_date season6_end_date + analyse_dataset_infants_further_overall_and_all_cause_ses_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_infants_2021_2022_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_covid_s6_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R infants season6_start_date - season6_end_date specific secondary infants s6 2021_2022 specific secondary - season6_start_date season6_end_date + analyse_dataset_infants_further_flu_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/covid_model_outputs_infants_2021_2022_specific_secondary.csv + csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_covid_further_s6_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R infants season6_start_date - season6_end_date specific secondary infants s6 2021_2022 specific secondary - season6_start_date season6_end_date + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_infants_2021_2022_specific_secondary.csv - - generate_dataset_infants_s7_specific_secondary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2022_2023_specific_secondary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow - -- infants season7_start_date season7_end_date specific secondary infants s7 2022_2023 specific secondary season7_start_date season7_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2022_2023_specific_secondary.arrow + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - process_dataset_infants_s7_specific_secondary: - run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date - specific secondary infants s7 2022_2023 specific secondary season7_start_date - season7_end_date + analyse_dataset_infants_further_flu_ethnicity_ses_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants + season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - generate_dataset_infants_s7_specific_secondary - - process_household_information_s7 + - process_dataset_infants_s3_specific_secondary outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2022_2023_specific_secondary.arrow + moderately_sensitive: + csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_secondary.csv - describe_dataset_infants_s7_specific_secondary: - run: r:latest analysis/report.R infants season7_start_date season7_end_date specific - secondary infants s7 2022_2023 specific secondary season7_start_date season7_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/rates/rates_infants_2022_2023_specific_secondary.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_rsv_s7_specific_secondary: - run: r:latest analysis/outcome_rsv/rsv_models.R infants season7_start_date season7_end_date - specific secondary infants s7 2022_2023 specific secondary season7_start_date - season7_end_date + analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants + season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/*_infants_2022_2023_specific_*.csv + csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_rsv_further_s7_specific_secondary: - run: r:latest analysis/outcome_rsv/further_rsv_models.R infants season7_start_date - season7_end_date specific secondary infants s7 2022_2023 specific secondary - season7_start_date season7_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/rsv_secondary/further_*_infants_2022_2023_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_flu_s7_specific_secondary: - run: r:latest analysis/outcome_flu/flu_models.R infants season7_start_date season7_end_date - specific secondary infants s7 2022_2023 specific secondary season7_start_date - season7_end_date + analyse_dataset_infants_further_flu_ses_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/*_infants_2022_2023_specific_*.csv + csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_flu_further_s7_specific_secondary: - run: r:latest analysis/outcome_flu/further_flu_models.R infants season7_start_date - season7_end_date specific secondary infants s7 2022_2023 specific secondary - season7_start_date season7_end_date + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/flu_secondary/further_*_infants_2022_2023_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models.R - infants season7_start_date season7_end_date specific secondary infants s7 2022_2023 - specific secondary season7_start_date season7_end_date + analyse_dataset_infants_further_flu_full_s3_specific_secondary: + run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season3_start_date + season3_end_date specific secondary infants s3 2018_2019 specific secondary + season3_start_date season3_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/*_infants_2022_2023_specific_*.csv + csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_overall_and_all_cause_further_s7_specific_secondary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models.R - infants season7_start_date season7_end_date specific secondary infants s7 2022_2023 - specific secondary season7_start_date season7_end_date + analyse_dataset_infants_further_overall_and_all_cause_full_s3_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R + infants season3_start_date season3_end_date specific secondary infants s3 2018_2019 + specific secondary season3_start_date season3_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s3_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_infants_2022_2023_specific_*.csv + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_secondary.csv - analyse_dataset_infants_covid_s7_specific_secondary: - run: r:latest analysis/outcome_covid/covid_models.R infants season7_start_date - season7_end_date specific secondary infants s7 2022_2023 specific secondary - season7_start_date season7_end_date + process_dataset_infants_s5_specific_secondary: + run: r:latest analysis/secondary_analyses/data_processing_sec.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_infants_s7_specific_secondary + - generate_dataset_infants_s5_specific_secondary + - process_household_information_s5 outputs: - moderately_sensitive: - csv: output/results/models/covid_model_outputs_infants_2022_2023_specific_secondary.csv + highly_sensitive: + cohort: output/data/input_processed_infants_s5_specific_secondary.arrow - analyse_dataset_infants_covid_further_s7_specific_secondary: - run: r:latest analysis/outcome_covid/further_covid_models.R infants season7_start_date - season7_end_date specific secondary infants s7 2022_2023 specific secondary - season7_start_date season7_end_date + describe_dataset_infants_s5_specific_secondary: + run: r:latest analysis/report.R infants season5_start_date season5_end_date specific + secondary infants s5 2020_2021 specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_model_outputs_infants_2022_2023_specific_secondary.csv - - ## # # # # # # # # # # # # # # # # # # # - ## DESCRIPTIVE ANALYSES - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Older Adults - ## # # # # # # # # # # # # # # # # # # # + csv: output/results/rates/rates_infants_s5_specific_secondary.csv - describe_cohort_older_adults_s1: - run: r:latest analysis/cohort_description.R older_adults season1_start_date season1_end_date - specific secondary older_adults s1 2016_2017 specific secondary season1_start_date - season1_end_date + analyse_dataset_infants_covid_ethnicity_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_older_adults_s1_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2016_2017.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_older_adults_s2: - run: r:latest analysis/cohort_description.R older_adults season2_start_date season2_end_date - specific secondary older_adults s2 2017_2018 specific secondary season2_start_date - season2_end_date + analyse_dataset_infants_covid_ses_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_older_adults_s2_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2017_2018.csv + csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_older_adults_s3: - run: r:latest analysis/cohort_description.R older_adults season3_start_date season3_end_date - specific secondary older_adults s3 2018_2019 specific secondary season3_start_date - season3_end_date + analyse_dataset_infants_covid_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_older_adults_s3_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2018_2019.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_older_adults_s4: - run: r:latest analysis/cohort_description.R older_adults season4_start_date season4_end_date - specific secondary older_adults s4 2019_2020 specific secondary season4_start_date - season4_end_date + analyse_dataset_infants_covid_ethnicity_ses_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_older_adults_s4_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2019_2020.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_older_adults_s5: - run: r:latest analysis/cohort_description.R older_adults season5_start_date season5_end_date - specific secondary older_adults s5 2020_2021 specific secondary season5_start_date - season5_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_older_adults_s5_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2020_2021.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_older_adults_s6: - run: r:latest analysis/cohort_description.R older_adults season6_start_date season6_end_date - specific secondary older_adults s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_infants_covid_ses_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_older_adults_s6_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2021_2022.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_older_adults_s7: - run: r:latest analysis/cohort_description.R older_adults season7_start_date season7_end_date - specific secondary older_adults s7 2022_2023 specific secondary season7_start_date - season7_end_date + analyse_dataset_infants_covid_full_s5_specific_secondary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_older_adults_s7_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_older_adults_2022_2023.csv - - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Adults - ## # # # # # # # # # # # # # # # # # # # + csv: output/results/models/covid_full_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_adults_s1: - run: r:latest analysis/cohort_description.R adults season1_start_date season1_end_date - specific secondary adults s1 2016_2017 specific secondary season1_start_date - season1_end_date + analyse_dataset_infants_further_covid_ethnicity_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants + season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_adults_s1_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2016_2017.csv + csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_adults_s2: - run: r:latest analysis/cohort_description.R adults season2_start_date season2_end_date - specific secondary adults s2 2017_2018 specific secondary season2_start_date - season2_end_date + analyse_dataset_infantsfurther__covid_ses_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_adults_s2_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2017_2018.csv + csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_adults_s3: - run: r:latest analysis/cohort_description.R adults season3_start_date season3_end_date - specific secondary adults s3 2018_2019 specific secondary season3_start_date - season3_end_date + analyse_dataset_infants_further_covid_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_adults_s3_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2018_2019.csv + csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_adults_s4: - run: r:latest analysis/cohort_description.R adults season4_start_date season4_end_date - specific secondary adults s4 2019_2020 specific secondary season4_start_date - season4_end_date + analyse_dataset_infants_further_covid_ethnicity_ses_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants + season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_adults_s4_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2019_2020.csv + csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_adults_s5: - run: r:latest analysis/cohort_description.R adults season5_start_date season5_end_date - specific secondary adults s5 2020_2021 specific secondary season5_start_date - season5_end_date + analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_adults_s5_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2020_2021.csv + csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_adults_s6: - run: r:latest analysis/cohort_description.R adults season6_start_date season6_end_date - specific secondary adults s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_infants_further_covid_ses_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants + season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_adults_s6_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2021_2022.csv + csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_adults_s7: - run: r:latest analysis/cohort_description.R adults season7_start_date season7_end_date - specific secondary adults s7 2022_2023 specific secondary season7_start_date - season7_end_date + analyse_dataset_infants_further_covid_full_s5_specific_secondary: + run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season5_start_date + season5_end_date specific secondary infants s5 2020_2021 specific secondary + season5_start_date season5_end_date needs: - - process_dataset_adults_s7_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_adults_2022_2023.csv - - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Children and Adolescents - ## # # # # # # # # # # # # # # # # # # # + csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_children_and_adolescents_s1: - run: r:latest analysis/cohort_description.R children_and_adolescents season1_start_date - season1_end_date specific secondary children_and_adolescents s1 2016_2017 specific - secondary season1_start_date season1_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s1_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2016_2017.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_children_and_adolescents_s2: - run: r:latest analysis/cohort_description.R children_and_adolescents season2_start_date - season2_end_date specific secondary children_and_adolescents s2 2017_2018 specific - secondary season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_ses_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s2_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2017_2018.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_children_and_adolescents_s3: - run: r:latest analysis/cohort_description.R children_and_adolescents season3_start_date - season3_end_date specific secondary children_and_adolescents s3 2018_2019 specific - secondary season3_start_date season3_end_date + analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s3_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2018_2019.csv + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_children_and_adolescents_s4: - run: r:latest analysis/cohort_description.R children_and_adolescents season4_start_date - season4_end_date specific secondary children_and_adolescents s4 2019_2020 specific - secondary season4_start_date season4_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s4_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2019_2020.csv + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_children_and_adolescents_s5: - run: r:latest analysis/cohort_description.R children_and_adolescents season5_start_date - season5_end_date specific secondary children_and_adolescents s5 2020_2021 specific - secondary season5_start_date season5_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s5_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2020_2021.csv + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_children_and_adolescents_s6: - run: r:latest analysis/cohort_description.R children_and_adolescents season6_start_date - season6_end_date specific secondary children_and_adolescents s6 2021_2022 specific - secondary season6_start_date season6_end_date + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s6_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2021_2022.csv + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_children_and_adolescents_s7: - run: r:latest analysis/cohort_description.R children_and_adolescents season7_start_date - season7_end_date specific secondary children_and_adolescents s7 2022_2023 specific - secondary season7_start_date season7_end_date + analyse_dataset_infants_overall_and_all_cause_full_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_children_and_adolescents_s7_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_children_and_adolescents_2022_2023.csv - - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Infants - ## # # # # # # # # # # # # # # # # # # # + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_infants_s1: - run: r:latest analysis/cohort_description.R infants season1_start_date season1_end_date - specific secondary infants s1 2016_2017 specific secondary season1_start_date - season1_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s1_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2016_2017.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_infants_s2: - run: r:latest analysis/cohort_description.R infants season2_start_date season2_end_date - specific secondary infants s2 2017_2018 specific secondary season2_start_date - season2_end_date + analyse_dataset_infantsfurther__overall_and_all_cause_ses_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s2_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2017_2018.csv + csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_infants_s3: - run: r:latest analysis/cohort_description.R infants season3_start_date season3_end_date - specific secondary infants s3 2018_2019 specific secondary season3_start_date - season3_end_date + analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s3_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2018_2019.csv + csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_infants_s4: - run: r:latest analysis/cohort_description.R infants season4_start_date season4_end_date - specific secondary infants s4 2019_2020 specific secondary season4_start_date - season4_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2019_2020.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_infants_s5: - run: r:latest analysis/cohort_description.R infants season5_start_date season5_end_date - specific secondary infants s5 2020_2021 specific secondary season5_start_date - season5_end_date + analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2020_2021.csv + csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_infants_s6: - run: r:latest analysis/cohort_description.R infants season6_start_date season6_end_date - specific secondary infants s6 2021_2022 specific secondary season6_start_date - season6_end_date + analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s6_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2021_2022.csv + csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - describe_cohort_infants_s7: - run: r:latest analysis/cohort_description.R infants season7_start_date season7_end_date - specific secondary infants s7 2022_2023 specific secondary season7_start_date - season7_end_date + analyse_dataset_infants_further_overall_and_all_cause_full_s5_specific_secondary: + run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R + infants season5_start_date season5_end_date specific secondary infants s5 2020_2021 + specific secondary season5_start_date season5_end_date needs: - - process_dataset_infants_s7_specific_secondary + - process_dataset_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/table1/table1_infants_2022_2023.csv + csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_secondary.csv ## # # # # # # # # # # # # # # # # # # # ## EXPLORATORY ANALYSES @@ -27186,13 +26358,9 @@ actions: run: r:latest analysis/collation_code/rates_table_specific_secondary_collation.R older_adults older_adults needs: - - describe_dataset_older_adults_s1_specific_secondary - describe_dataset_older_adults_s2_specific_secondary - describe_dataset_older_adults_s3_specific_secondary - - describe_dataset_older_adults_s4_specific_secondary - describe_dataset_older_adults_s5_specific_secondary - - describe_dataset_older_adults_s6_specific_secondary - - describe_dataset_older_adults_s7_specific_secondary outputs: moderately_sensitive: csv: output/collated/descriptive/older_adults_rates_specific_secondary_collated.csv @@ -27287,7 +26455,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/older_adults_covid_model_outputs_collated.csv - collate_overall_and_all_cause_model_outputs_tables_older_adults: + collate_overall_and_all_cause_outputs_tables_older_adults: run: r:latest analysis/collation_code/overall_and_all_cause_model_outputs_table_collation.R older_adults older_adults needs: @@ -27309,6 +26477,42 @@ actions: moderately_sensitive: csv: output/collated/analytic/older_adults_overall_and_all_cause_model_outputs_collated.csv + collate_rsv_outputs_tables_older_adults_secondary: + run: r:latest analysis/collation_code/rsv_outputs_table_collation_secondary.R + older_adults older_adults + needs: + - analyse_dataset_older_adults_rsv_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/older_adults_rsv_model_outputs_collated_secondary.csv + + collate_flu_outputs_tables_older_adults_secondary: + run: r:latest analysis/collation_code/flu_outputs_table_collation_secondary.R + older_adults older_adults + needs: + - analyse_dataset_older_adults_flu_s3_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/older_adults_flu_model_outputs_collated_secondary.csv + + collate_covid_outputs_tables_older_adults_secondary: + run: r:latest analysis/collation_code/covid_outputs_table_collation_secondary.R + older_adults older_adults + needs: + - analyse_dataset_older_adults_covid_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/older_adults_covid_model_outputs_collated_secondary.csv + + collate_overall_and_all_cause_outputs_tables_older_adults_secondary: + run: r:latest analysis/collation_code/overall_and_all_cause_outputs_table_collation_secondary.R + older_adults older_adults + needs: + - analyse_dataset_older_adults_overall_and_all_cause_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/older_adults_overall_and_all_cause_model_outputs_collated_secondary.csv + collate_rsv_outputs_tables_older_adults_sensitivity: run: r:latest analysis/collation_code/rsv_outputs_table_collation_sensitivity.R older_adults older_adults @@ -27329,7 +26533,7 @@ actions: - analyse_dataset_older_adults_rsv_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/older_adults_rsv_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/older_adults_rsv_model_outputs_collated_sensitivity.csv collate_flu_outputs_tables_older_adults_sensitivity: run: r:latest analysis/collation_code/flu_outputs_table_collation_sensitivity.R @@ -27351,7 +26555,7 @@ actions: - analyse_dataset_older_adults_flu_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/older_adults_flu_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/older_adults_flu_model_outputs_collated_sensitivity.csv collate_covid_outputs_tables_older_adults_sensitivity: run: r:latest analysis/collation_code/covid_outputs_table_collation_sensitivity.R @@ -27367,7 +26571,7 @@ actions: - analyse_dataset_older_adults_covid_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/older_adults_covid_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/older_adults_covid_model_outputs_collated_sensitivity.csv collate_overall_and_all_cause_outputs_tables_older_adults_sensitivity: run: r:latest analysis/collation_code/overall_and_all_cause_outputs_table_collation_sensitivity.R @@ -27389,7 +26593,7 @@ actions: - analyse_dataset_older_adults_overall_and_all_cause_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/older_adults_overall_and_all_cause_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/older_adults_overall_and_all_cause_model_outputs_collated_sensitivity.csv collate_flow_chart_tables_adults: run: r:latest analysis/collation_code/flow_chart_table_collation.R adults adults @@ -27453,13 +26657,9 @@ actions: run: r:latest analysis/collation_code/rates_table_specific_secondary_collation.R adults adults needs: - - describe_dataset_adults_s1_specific_secondary - describe_dataset_adults_s2_specific_secondary - describe_dataset_adults_s3_specific_secondary - - describe_dataset_adults_s4_specific_secondary - describe_dataset_adults_s5_specific_secondary - - describe_dataset_adults_s6_specific_secondary - - describe_dataset_adults_s7_specific_secondary outputs: moderately_sensitive: csv: output/collated/descriptive/adults_rates_specific_secondary_collated.csv @@ -27554,7 +26754,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/adults_covid_model_outputs_collated.csv - collate_overall_and_all_cause_model_outputs_tables_adults: + collate_overall_and_all_cause_outputs_tables_adults: run: r:latest analysis/collation_code/overall_and_all_cause_model_outputs_table_collation.R adults adults needs: @@ -27576,6 +26776,42 @@ actions: moderately_sensitive: csv: output/collated/analytic/adults_overall_and_all_cause_model_outputs_collated.csv + collate_rsv_outputs_tables_adults_secondary: + run: r:latest analysis/collation_code/rsv_outputs_table_collation_secondary.R + adults adults + needs: + - analyse_dataset_adults_rsv_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/adults_rsv_model_outputs_collated_secondary.csv + + collate_flu_outputs_tables_adults_secondary: + run: r:latest analysis/collation_code/flu_outputs_table_collation_secondary.R + adults adults + needs: + - analyse_dataset_adults_flu_s3_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/adults_flu_model_outputs_collated_secondary.csv + + collate_covid_outputs_tables_adults_secondary: + run: r:latest analysis/collation_code/covid_outputs_table_collation_secondary.R + adults adults + needs: + - analyse_dataset_adults_covid_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/adults_covid_model_outputs_collated_secondary.csv + + collate_overall_and_all_cause_outputs_tables_adults_secondary: + run: r:latest analysis/collation_code/overall_and_all_cause_outputs_table_collation_secondary.R + adults adults + needs: + - analyse_dataset_adults_overall_and_all_cause_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/adults_overall_and_all_cause_model_outputs_collated_secondary.csv + collate_rsv_outputs_tables_adults_sensitivity: run: r:latest analysis/collation_code/rsv_outputs_table_collation_sensitivity.R adults adults @@ -27596,7 +26832,7 @@ actions: - analyse_dataset_adults_rsv_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/adults_rsv_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/adults_rsv_model_outputs_collated_sensitivity.csv collate_flu_outputs_tables_adults_sensitivity: run: r:latest analysis/collation_code/flu_outputs_table_collation_sensitivity.R @@ -27618,7 +26854,7 @@ actions: - analyse_dataset_adults_flu_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/adults_flu_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/adults_flu_model_outputs_collated_sensitivity.csv collate_covid_outputs_tables_adults_sensitivity: run: r:latest analysis/collation_code/covid_outputs_table_collation_sensitivity.R @@ -27634,7 +26870,7 @@ actions: - analyse_dataset_adults_covid_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/adults_covid_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/adults_covid_model_outputs_collated_sensitivity.csv collate_overall_and_all_cause_outputs_tables_adults_sensitivity: run: r:latest analysis/collation_code/overall_and_all_cause_outputs_table_collation_sensitivity.R @@ -27656,7 +26892,7 @@ actions: - analyse_dataset_adults_overall_and_all_cause_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/adults_overall_and_all_cause_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/adults_overall_and_all_cause_model_outputs_collated_sensitivity.csv collate_flow_chart_tables_children_and_adolescents: run: r:latest analysis/collation_code/flow_chart_table_collation.R children_and_adolescents @@ -27722,13 +26958,9 @@ actions: run: r:latest analysis/collation_code/rates_table_specific_secondary_collation.R children_and_adolescents children_and_adolescents needs: - - describe_dataset_children_and_adolescents_s1_specific_secondary - describe_dataset_children_and_adolescents_s2_specific_secondary - describe_dataset_children_and_adolescents_s3_specific_secondary - - describe_dataset_children_and_adolescents_s4_specific_secondary - describe_dataset_children_and_adolescents_s5_specific_secondary - - describe_dataset_children_and_adolescents_s6_specific_secondary - - describe_dataset_children_and_adolescents_s7_specific_secondary outputs: moderately_sensitive: csv: output/collated/descriptive/children_and_adolescents_rates_specific_secondary_collated.csv @@ -27823,7 +27055,7 @@ actions: moderately_sensitive: csv: output/collated/analytic/children_and_adolescents_covid_model_outputs_collated.csv - collate_overall_and_all_cause_model_outputs_tables_children_and_adolescents: + collate_overall_and_all_cause_outputs_tables_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: @@ -27845,6 +27077,42 @@ actions: moderately_sensitive: csv: output/collated/analytic/children_and_adolescents_overall_and_all_cause_model_outputs_collated.csv + collate_rsv_outputs_tables_children_and_adolescents_secondary: + run: r:latest analysis/collation_code/rsv_outputs_table_collation_secondary.R + children_and_adolescents children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_rsv_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/children_and_adolescents_rsv_model_outputs_collated_secondary.csv + + collate_flu_outputs_tables_children_and_adolescents_secondary: + run: r:latest analysis/collation_code/flu_outputs_table_collation_secondary.R + children_and_adolescents children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_flu_s3_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/children_and_adolescents_flu_model_outputs_collated_secondary.csv + + collate_covid_outputs_tables_children_and_adolescents_secondary: + run: r:latest analysis/collation_code/covid_outputs_table_collation_secondary.R + children_and_adolescents children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_covid_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/children_and_adolescents_covid_model_outputs_collated_secondary.csv + + collate_overall_and_all_cause_outputs_tables_children_and_adolescents_secondary: + run: r:latest analysis/collation_code/overall_and_all_cause_outputs_table_collation_secondary.R + children_and_adolescents children_and_adolescents + needs: + - analyse_dataset_children_and_adolescents_overall_and_all_cause_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/secondary/children_and_adolescents_overall_and_all_cause_model_outputs_collated_secondary.csv + collate_rsv_outputs_tables_children_and_adolescents_sensitivity: run: r:latest analysis/collation_code/rsv_outputs_table_collation_sensitivity.R children_and_adolescents children_and_adolescents @@ -27865,7 +27133,7 @@ actions: - analyse_dataset_children_and_adolescents_rsv_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/children_and_adolescents_rsv_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/children_and_adolescents_rsv_model_outputs_collated_sensitivity.csv collate_flu_outputs_tables_children_and_adolescents_sensitivity: run: r:latest analysis/collation_code/flu_outputs_table_collation_sensitivity.R @@ -27887,7 +27155,7 @@ actions: - analyse_dataset_children_and_adolescents_flu_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/children_and_adolescents_flu_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/children_and_adolescents_flu_model_outputs_collated_sensitivity.csv collate_covid_outputs_tables_children_and_adolescents_sensitivity: run: r:latest analysis/collation_code/covid_outputs_table_collation_sensitivity.R @@ -27903,7 +27171,7 @@ actions: - analyse_dataset_children_and_adolescents_covid_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/children_and_adolescents_covid_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/children_and_adolescents_covid_model_outputs_collated_sensitivity.csv collate_overall_and_all_cause_outputs_tables_children_and_adolescents_sensitivity: run: r:latest analysis/collation_code/overall_and_all_cause_outputs_table_collation_sensitivity.R @@ -27925,7 +27193,7 @@ actions: - analyse_dataset_children_and_adolescents_overall_and_all_cause_s7_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/collated/analytic/children_and_adolescents_overall_and_all_cause_model_outputs_collated_sensitivity.csv + csv: output/collated/analytic/sensitivity/children_and_adolescents_overall_and_all_cause_model_outputs_collated_sensitivity.csv collate_flow_chart_tables_infants: run: r:latest analysis/collation_code/flow_chart_table_collation.R infants infants @@ -27989,13 +27257,9 @@ actions: run: r:latest analysis/collation_code/rates_table_specific_secondary_collation.R infants infants needs: - - describe_dataset_infants_s1_specific_secondary - describe_dataset_infants_s2_specific_secondary - describe_dataset_infants_s3_specific_secondary - - describe_dataset_infants_s4_specific_secondary - describe_dataset_infants_s5_specific_secondary - - describe_dataset_infants_s6_specific_secondary - - describe_dataset_infants_s7_specific_secondary outputs: moderately_sensitive: csv: output/collated/descriptive/infants_rates_specific_secondary_collated.csv @@ -28412,6 +27676,66 @@ actions: moderately_sensitive: csv: output/collated/analytic/infants_overall_and_all_cause_model_outputs_collated.csv + collate_rsv_model_outputs_tables_infants_secondary: + run: r:latest analysis/collation_code/rsv_model_outputs_table_collation_secondary.R + infants infants + needs: + - analyse_dataset_infants_rsv_ethnicity_s2_specific_secondary + - analyse_dataset_infants_rsv_ses_s2_specific_secondary + - analyse_dataset_infants_rsv_hh_comp_s2_specific_secondary + - analyse_dataset_infants_rsv_ethnicity_ses_s2_specific_secondary + - analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_specific_secondary + - analyse_dataset_infants_rsv_ses_hh_comp_s2_specific_secondary + - analyse_dataset_infants_rsv_full_s2_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/infants_rsv_model_outputs_secondary_collated.csv + + collate_flu_model_outputs_tables_infants_secondary: + run: r:latest analysis/collation_code/flu_model_outputs_table_collation_secondary.R + infants infants + needs: + - analyse_dataset_infants_flu_ethnicity_s3_specific_secondary + - analyse_dataset_infants_flu_ses_s3_specific_secondary + - analyse_dataset_infants_flu_hh_comp_s3_specific_secondary + - analyse_dataset_infants_flu_ethnicity_ses_s3_specific_secondary + - analyse_dataset_infants_flu_ethnicity_hh_comp_s3_specific_secondary + - analyse_dataset_infants_flu_ses_hh_comp_s3_specific_secondary + - analyse_dataset_infants_flu_full_s3_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/infants_flu_model_outputs_secondary_collated.csv + + collate_covid_model_outputs_tables_infants_secondary: + run: r:latest analysis/collation_code/covid_model_outputs_table_collation_secondary.R + infants infants + needs: + - analyse_dataset_infants_covid_ethnicity_s5_specific_secondary + - analyse_dataset_infants_covid_ses_s5_specific_secondary + - analyse_dataset_infants_covid_hh_comp_s5_specific_secondary + - analyse_dataset_infants_covid_ethnicity_ses_s5_specific_secondary + - analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_secondary + - analyse_dataset_infants_covid_ses_hh_comp_s5_specific_secondary + - analyse_dataset_infants_covid_full_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/infants_covid_model_outputs_secondary_collated.csv + + collate_overall_and_all_cause_model_outputs_tables_infants_secondary: + run: r:latest analysis/collation_code/overall_and_all_cause_model_outputs_table_collation_secondary.R + infants infants + needs: + - analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_secondary + - analyse_dataset_infants_overall_and_all_cause_ses_s5_specific_secondary + - analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_specific_secondary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_specific_secondary + - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_specific_secondary + - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_specific_secondary + - analyse_dataset_infants_overall_and_all_cause_full_s5_specific_secondary + outputs: + moderately_sensitive: + csv: output/collated/analytic/infants_overall_and_all_cause_model_outputs_secondary_collated.csv + collate_phenotype_sensitivity_tables_infants: run: r:latest analysis/collation_code/phenotype_sensitivity_table_collation.R infants infants