From 007df3a07bd3ebf0d6224d29af3d91e895a1f431 Mon Sep 17 00:00:00 2001 From: Em Prestige Date: Mon, 30 Sep 2024 12:00:54 +0100 Subject: [PATCH] update yaml --- actions.txt | 40 +- create-project.R | 1846 ++++---- project.yaml | 10819 +++++---------------------------------------- 3 files changed, 1812 insertions(+), 10893 deletions(-) diff --git a/actions.txt b/actions.txt index 1fce0bc..5cd5f96 100644 --- a/actions.txt +++ b/actions.txt @@ -3,33 +3,33 @@ generate_flow_chart_data_adults_s1 process_flow_chart_data_adults_s1 generate_fl generate_flow_chart_data_children_and_adolescents_s1 process_flow_chart_data_children_and_adolescents_s1 generate_flow_chart_data_children_and_adolescents_s2 process_flow_chart_data_children_and_adolescents_s2 generate_flow_chart_data_children_and_adolescents_s3 process_flow_chart_data_children_and_adolescents_s3 generate_flow_chart_data_children_and_adolescents_s4 process_flow_chart_data_children_and_adolescents_s4 generate_flow_chart_data_children_and_adolescents_s5 process_flow_chart_data_children_and_adolescents_s5 generate_flow_chart_data_children_and_adolescents_s6 process_flow_chart_data_children_and_adolescents_s6 generate_flow_chart_data_children_and_adolescents_s7 process_flow_chart_data_children_and_adolescents_s7 generate_flow_chart_data_infants_s1 process_flow_chart_data_infants_s1 generate_flow_chart_data_infants_s2 process_flow_chart_data_infants_s2 generate_flow_chart_data_infants_s3 process_flow_chart_data_infants_s3 generate_flow_chart_data_infants_s4 process_flow_chart_data_infants_s4 generate_flow_chart_data_infants_s5 process_flow_chart_data_infants_s5 generate_flow_chart_data_infants_s6 process_flow_chart_data_infants_s6 generate_flow_chart_data_infants_s7 process_flow_chart_data_infants_s7 extract_household_information_s1 process_household_information_s1 extract_household_information_s2 process_household_information_s2 extract_household_information_s3 process_household_information_s3 extract_household_information_s4 process_household_information_s4 extract_household_information_s5 process_household_information_s5 extract_household_information_s6 process_household_information_s6 extract_household_information_s7 process_household_information_s7 -generate_dataset_older_adults_s1_specific_primary process_dataset_older_adults_s1_specific_primary describe_dataset_older_adults_s1_specific_primary analyse_dataset_older_adults_rsv_s1_specific_primary analyse_dataset_older_adults_rsv_further_s1_specific_primary analyse_dataset_older_adults_flu_s1_specific_primary analyse_dataset_older_adults_flu_further_s1_specific_primary analyse_dataset_older_adults_overall_and_all_cause_s1_specific_primary analyse_dataset_older_adults_overall_and_all_cause_further_s1_specific_primary generate_dataset_older_adults_s2_specific_primary process_dataset_older_adults_s2_specific_primary describe_dataset_older_adults_s2_specific_primary analyse_dataset_older_adults_rsv_s2_specific_primary analyse_dataset_older_adults_rsv_further_s2_specific_primary analyse_dataset_older_adults_flu_s2_specific_primary analyse_dataset_older_adults_flu_further_s2_specific_primary analyse_dataset_older_adults_overall_and_all_cause_s2_specific_primary analyse_dataset_older_adults_overall_and_all_cause_further_s2_specific_primary generate_dataset_older_adults_s3_specific_primary process_dataset_older_adults_s3_specific_primary describe_dataset_older_adults_s3_specific_primary analyse_dataset_older_adults_rsv_s3_specific_primary analyse_dataset_older_adults_rsv_further_s3_specific_primary analyse_dataset_older_adults_flu_s3_specific_primary analyse_dataset_older_adults_flu_further_s3_specific_primary analyse_dataset_older_adults_overall_and_all_cause_s3_specific_primary analyse_dataset_older_adults_overall_and_all_cause_further_s3_specific_primary generate_dataset_older_adults_s4_specific_primary process_dataset_older_adults_s4_specific_primary describe_dataset_older_adults_s4_specific_primary analyse_dataset_older_adults_rsv_s4_specific_primary analyse_dataset_older_adults_rsv_further_s4_specific_primary analyse_dataset_older_adults_flu_s4_specific_primary analyse_dataset_older_adults_flu_further_s4_specific_primary analyse_dataset_older_adults_overall_and_all_cause_s4_specific_primary analyse_dataset_older_adults_overall_and_all_cause_further_s4_specific_primary analyse_dataset_older_adults_covid_s4_specific_primary analyse_dataset_older_adults_covid_further_s4_specific_primary generate_dataset_older_adults_s5_specific_primary process_dataset_older_adults_s5_specific_primary describe_dataset_older_adults_s5_specific_primary analyse_dataset_older_adults_rsv_s5_specific_primary analyse_dataset_older_adults_rsv_further_s5_specific_primary analyse_dataset_older_adults_flu_s5_specific_primary analyse_dataset_older_adults_flu_further_s5_specific_primary analyse_dataset_older_adults_overall_and_all_cause_s5_specific_primary analyse_dataset_older_adults_overall_and_all_cause_further_s5_specific_primary analyse_dataset_older_adults_covid_s5_specific_primary analyse_dataset_older_adults_covid_further_s5_specific_primary generate_dataset_older_adults_s6_specific_primary process_dataset_older_adults_s6_specific_primary describe_dataset_older_adults_s6_specific_primary analyse_dataset_older_adults_rsv_s6_specific_primary analyse_dataset_older_adults_rsv_further_s6_specific_primary analyse_dataset_older_adults_flu_s6_specific_primary analyse_dataset_older_adults_flu_further_s6_specific_primary analyse_dataset_older_adults_overall_and_all_cause_s6_specific_primary analyse_dataset_older_adults_overall_and_all_cause_further_s6_specific_primary analyse_dataset_older_adults_covid_s6_specific_primary analyse_dataset_older_adults_covid_further_s6_specific_primary generate_dataset_older_adults_s7_specific_primary process_dataset_older_adults_s7_specific_primary describe_dataset_older_adults_s7_specific_primary analyse_dataset_older_adults_rsv_s7_specific_primary analyse_dataset_older_adults_rsv_further_s7_specific_primary analyse_dataset_older_adults_flu_s7_specific_primary analyse_dataset_older_adults_flu_further_s7_specific_primary analyse_dataset_older_adults_overall_and_all_cause_s7_specific_primary analyse_dataset_older_adults_overall_and_all_cause_further_s7_specific_primary analyse_dataset_older_adults_covid_s7_specific_primary analyse_dataset_older_adults_covid_further_s7_specific_primary -generate_dataset_adults_s1_specific_primary process_dataset_adults_s1_specific_primary describe_dataset_adults_s1_specific_primary analyse_dataset_adults_rsv_s1_specific_primary analyse_dataset_adults_rsv_further_s1_specific_primary analyse_dataset_adults_flu_s1_specific_primary analyse_dataset_adults_flu_further_s1_specific_primary analyse_dataset_adults_overall_and_all_cause_s1_specific_primary analyse_dataset_adults_overall_and_all_cause_further_s1_specific_primary generate_dataset_adults_s2_specific_primary process_dataset_adults_s2_specific_primary describe_dataset_adults_s2_specific_primary analyse_dataset_adults_rsv_s2_specific_primary analyse_dataset_adults_rsv_further_s2_specific_primary analyse_dataset_adults_flu_s2_specific_primary analyse_dataset_adults_flu_further_s2_specific_primary analyse_dataset_adults_overall_and_all_cause_s2_specific_primary analyse_dataset_adults_overall_and_all_cause_further_s2_specific_primary generate_dataset_adults_s3_specific_primary process_dataset_adults_s3_specific_primary describe_dataset_adults_s3_specific_primary analyse_dataset_adults_rsv_s3_specific_primary analyse_dataset_adults_rsv_further_s3_specific_primary analyse_dataset_adults_flu_s3_specific_primary analyse_dataset_adults_flu_further_s3_specific_primary analyse_dataset_adults_overall_and_all_cause_s3_specific_primary analyse_dataset_adults_overall_and_all_cause_further_s3_specific_primary generate_dataset_adults_s4_specific_primary process_dataset_adults_s4_specific_primary describe_dataset_adults_s4_specific_primary analyse_dataset_adults_rsv_s4_specific_primary analyse_dataset_adults_rsv_further_s4_specific_primary analyse_dataset_adults_flu_s4_specific_primary analyse_dataset_adults_flu_further_s4_specific_primary analyse_dataset_adults_overall_and_all_cause_s4_specific_primary analyse_dataset_adults_overall_and_all_cause_further_s4_specific_primary analyse_dataset_adults_covid_s4_specific_primary analyse_dataset_adults_covid_further_s4_specific_primary generate_dataset_adults_s5_specific_primary process_dataset_adults_s5_specific_primary describe_dataset_adults_s5_specific_primary analyse_dataset_adults_rsv_s5_specific_primary analyse_dataset_adults_rsv_further_s5_specific_primary analyse_dataset_adults_flu_s5_specific_primary analyse_dataset_adults_flu_further_s5_specific_primary analyse_dataset_adults_overall_and_all_cause_s5_specific_primary analyse_dataset_adults_overall_and_all_cause_further_s5_specific_primary analyse_dataset_adults_covid_s5_specific_primary analyse_dataset_adults_covid_further_s5_specific_primary generate_dataset_adults_s6_specific_primary process_dataset_adults_s6_specific_primary describe_dataset_adults_s6_specific_primary analyse_dataset_adults_rsv_s6_specific_primary analyse_dataset_adults_rsv_further_s6_specific_primary analyse_dataset_adults_flu_s6_specific_primary analyse_dataset_adults_flu_further_s6_specific_primary analyse_dataset_adults_overall_and_all_cause_s6_specific_primary analyse_dataset_adults_overall_and_all_cause_further_s6_specific_primary analyse_dataset_adults_covid_s6_specific_primary analyse_dataset_adults_covid_further_s6_specific_primary generate_dataset_adults_s7_specific_primary process_dataset_adults_s7_specific_primary describe_dataset_adults_s7_specific_primary analyse_dataset_adults_rsv_s7_specific_primary analyse_dataset_adults_rsv_further_s7_specific_primary analyse_dataset_adults_flu_s7_specific_primary analyse_dataset_adults_flu_further_s7_specific_primary analyse_dataset_adults_overall_and_all_cause_s7_specific_primary analyse_dataset_adults_overall_and_all_cause_further_s7_specific_primary analyse_dataset_adults_covid_s7_specific_primary analyse_dataset_adults_covid_further_s7_specific_primary -generate_dataset_children_and_adolescents_s1_specific_primary process_dataset_children_and_adolescents_s1_specific_primary describe_dataset_children_and_adolescents_s1_specific_primary analyse_dataset_children_and_adolescents_rsv_s1_specific_primary analyse_dataset_children_and_adolescents_rsv_further_s1_specific_primary analyse_dataset_children_and_adolescents_flu_s1_specific_primary analyse_dataset_children_and_adolescents_flu_further_s1_specific_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_s1_specific_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s1_specific_primary generate_dataset_children_and_adolescents_s2_specific_primary process_dataset_children_and_adolescents_s2_specific_primary describe_dataset_children_and_adolescents_s2_specific_primary analyse_dataset_children_and_adolescents_rsv_s2_specific_primary analyse_dataset_children_and_adolescents_rsv_further_s2_specific_primary analyse_dataset_children_and_adolescents_flu_s2_specific_primary analyse_dataset_children_and_adolescents_flu_further_s2_specific_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_s2_specific_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_specific_primary generate_dataset_children_and_adolescents_s3_specific_primary process_dataset_children_and_adolescents_s3_specific_primary describe_dataset_children_and_adolescents_s3_specific_primary analyse_dataset_children_and_adolescents_rsv_s3_specific_primary 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process_dataset_infants_s5_specific_primary describe_dataset_infants_s5_specific_primary analyse_dataset_infants_rsv_ethnicity_s5_specific_primary analyse_dataset_infants_flu_ethnicity_s5_specific_primary analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_primary analyse_dataset_infants_rsv_ses_s5_specific_primary analyse_dataset_infants_flu_ses_s5_specific_primary analyse_dataset_infants_overall_and_all_cause_ses_s5_specific_primary analyse_dataset_infants_rsv_hh_comp_s5_specific_primary analyse_dataset_infants_flu_hh_comp_s5_specific_primary analyse_dataset_infants_overall_and_all_cause_hh_comp_s5_specific_primary analyse_dataset_infants_rsv_ethnicity_ses_s5_specific_primary analyse_dataset_infants_flu_ethnicity_ses_s5_specific_primary analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_specific_primary analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_specific_primary analyse_dataset_infants_flu_ethnicity_hh_comp_s5_specific_primary 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describe_dataset_older_adults_s1_sensitive_primary analyse_dataset_older_adults_rsv_s1_sensitive_primary analyse_dataset_older_adults_flu_s1_sensitive_primary analyse_dataset_older_adults_flu_further_s1_sensitive_primary analyse_dataset_older_adults_overall_and_all_cause_s1_sensitive_primary generate_dataset_older_adults_s2_sensitive_primary process_dataset_older_adults_s2_sensitive_primary describe_dataset_older_adults_s2_sensitive_primary analyse_dataset_older_adults_rsv_s2_sensitive_primary analyse_dataset_older_adults_flu_s2_sensitive_primary analyse_dataset_older_adults_flu_further_s2_sensitive_primary analyse_dataset_older_adults_overall_and_all_cause_s2_sensitive_primary generate_dataset_older_adults_s3_sensitive_primary process_dataset_older_adults_s3_sensitive_primary describe_dataset_older_adults_s3_sensitive_primary analyse_dataset_older_adults_rsv_s3_sensitive_primary analyse_dataset_older_adults_flu_s3_sensitive_primary analyse_dataset_older_adults_flu_further_s3_sensitive_primary analyse_dataset_older_adults_overall_and_all_cause_s3_sensitive_primary generate_dataset_older_adults_s4_sensitive_primary process_dataset_older_adults_s4_sensitive_primary describe_dataset_older_adults_s4_sensitive_primary analyse_dataset_older_adults_rsv_s4_sensitive_primary analyse_dataset_older_adults_flu_s4_sensitive_primary analyse_dataset_older_adults_flu_further_s4_sensitive_primary analyse_dataset_older_adults_overall_and_all_cause_s4_sensitive_primary analyse_dataset_older_adults_covid_s4_sensitive_primary analyse_dataset_older_adults_covid_further_s4_sensitive_primary generate_dataset_older_adults_s5_sensitive_primary process_dataset_older_adults_s5_sensitive_primary describe_dataset_older_adults_s5_sensitive_primary analyse_dataset_older_adults_rsv_s5_sensitive_primary analyse_dataset_older_adults_flu_s5_sensitive_primary analyse_dataset_older_adults_flu_further_s5_sensitive_primary analyse_dataset_older_adults_overall_and_all_cause_s5_sensitive_primary analyse_dataset_older_adults_covid_s5_sensitive_primary analyse_dataset_older_adults_covid_further_s5_sensitive_primary generate_dataset_older_adults_s6_sensitive_primary process_dataset_older_adults_s6_sensitive_primary describe_dataset_older_adults_s6_sensitive_primary analyse_dataset_older_adults_rsv_s6_sensitive_primary analyse_dataset_older_adults_flu_s6_sensitive_primary analyse_dataset_older_adults_flu_further_s6_sensitive_primary analyse_dataset_older_adults_overall_and_all_cause_s6_sensitive_primary analyse_dataset_older_adults_covid_s6_sensitive_primary analyse_dataset_older_adults_covid_further_s6_sensitive_primary generate_dataset_older_adults_s7_sensitive_primary process_dataset_older_adults_s7_sensitive_primary describe_dataset_older_adults_s7_sensitive_primary analyse_dataset_older_adults_rsv_s7_sensitive_primary analyse_dataset_older_adults_flu_s7_sensitive_primary analyse_dataset_older_adults_flu_further_s7_sensitive_primary analyse_dataset_older_adults_overall_and_all_cause_s7_sensitive_primary analyse_dataset_older_adults_covid_s7_sensitive_primary analyse_dataset_older_adults_covid_further_s7_sensitive_primary +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_flu_s1_sensitive_primary analyse_dataset_adults_flu_further_s1_sensitive_primary analyse_dataset_adults_overall_and_all_cause_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_flu_s2_sensitive_primary analyse_dataset_adults_flu_further_s2_sensitive_primary analyse_dataset_adults_overall_and_all_cause_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_flu_s3_sensitive_primary analyse_dataset_adults_flu_further_s3_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s3_sensitive_primary generate_dataset_adults_s4_sensitive_primary process_dataset_adults_s4_sensitive_primary describe_dataset_adults_s4_sensitive_primary analyse_dataset_adults_rsv_s4_sensitive_primary analyse_dataset_adults_flu_s4_sensitive_primary analyse_dataset_adults_flu_further_s4_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s4_sensitive_primary analyse_dataset_adults_covid_s4_sensitive_primary analyse_dataset_adults_covid_further_s4_sensitive_primary generate_dataset_adults_s5_sensitive_primary process_dataset_adults_s5_sensitive_primary describe_dataset_adults_s5_sensitive_primary analyse_dataset_adults_rsv_s5_sensitive_primary analyse_dataset_adults_flu_s5_sensitive_primary analyse_dataset_adults_flu_further_s5_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s5_sensitive_primary analyse_dataset_adults_covid_s5_sensitive_primary analyse_dataset_adults_covid_further_s5_sensitive_primary generate_dataset_adults_s6_sensitive_primary process_dataset_adults_s6_sensitive_primary describe_dataset_adults_s6_sensitive_primary analyse_dataset_adults_rsv_s6_sensitive_primary analyse_dataset_adults_flu_s6_sensitive_primary analyse_dataset_adults_flu_further_s6_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s6_sensitive_primary analyse_dataset_adults_covid_s6_sensitive_primary analyse_dataset_adults_covid_further_s6_sensitive_primary generate_dataset_adults_s7_sensitive_primary process_dataset_adults_s7_sensitive_primary describe_dataset_adults_s7_sensitive_primary analyse_dataset_adults_rsv_s7_sensitive_primary analyse_dataset_adults_flu_s7_sensitive_primary analyse_dataset_adults_flu_further_s7_sensitive_primary analyse_dataset_adults_overall_and_all_cause_s7_sensitive_primary analyse_dataset_adults_covid_s7_sensitive_primary analyse_dataset_adults_covid_further_s7_sensitive_primary +generate_dataset_children_and_adolescents_s1_sensitive_primary process_dataset_children_and_adolescents_s1_sensitive_primary describe_dataset_children_and_adolescents_s1_sensitive_primary analyse_dataset_children_and_adolescents_rsv_s1_sensitive_primary analyse_dataset_children_and_adolescents_flu_s1_sensitive_primary analyse_dataset_children_and_adolescents_flu_further_s1_sensitive_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_s1_sensitive_primary generate_dataset_children_and_adolescents_s2_sensitive_primary process_dataset_children_and_adolescents_s2_sensitive_primary describe_dataset_children_and_adolescents_s2_sensitive_primary analyse_dataset_children_and_adolescents_rsv_s2_sensitive_primary analyse_dataset_children_and_adolescents_flu_s2_sensitive_primary analyse_dataset_children_and_adolescents_flu_further_s2_sensitive_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_s2_sensitive_primary generate_dataset_children_and_adolescents_s3_sensitive_primary process_dataset_children_and_adolescents_s3_sensitive_primary describe_dataset_children_and_adolescents_s3_sensitive_primary analyse_dataset_children_and_adolescents_rsv_s3_sensitive_primary analyse_dataset_children_and_adolescents_flu_s3_sensitive_primary analyse_dataset_children_and_adolescents_flu_further_s3_sensitive_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_s3_sensitive_primary generate_dataset_children_and_adolescents_s4_sensitive_primary process_dataset_children_and_adolescents_s4_sensitive_primary describe_dataset_children_and_adolescents_s4_sensitive_primary analyse_dataset_children_and_adolescents_rsv_s4_sensitive_primary 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analyse_dataset_children_and_adolescents_flu_further_s7_sensitive_primary analyse_dataset_children_and_adolescents_overall_and_all_cause_s7_sensitive_primary analyse_dataset_children_and_adolescents_covid_s7_sensitive_primary analyse_dataset_children_and_adolescents_covid_further_s7_sensitive_primary +generate_dataset_infants_s1_sensitive_primary process_dataset_infants_s1_sensitive_primary describe_dataset_infants_s1_sensitive_primary analyse_dataset_infants_rsv_ethnicity_s1_sensitive_primary analyse_dataset_infants_flu_ethnicity_s1_sensitive_primary analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_sensitive_primary analyse_dataset_infants_rsv_ses_s1_sensitive_primary analyse_dataset_infants_flu_ses_s1_sensitive_primary analyse_dataset_infants_overall_and_all_cause_ses_s1_sensitive_primary analyse_dataset_infants_rsv_hh_comp_s1_sensitive_primary analyse_dataset_infants_flu_hh_comp_s1_sensitive_primary analyse_dataset_infants_overall_and_all_cause_hh_comp_s1_sensitive_primary 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analyse_dataset_adults_rsv_s5_sensitive_sensitivity analyse_dataset_adults_flu_s5_sensitive_sensitivity analyse_dataset_adults_flu_further_s5_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_s5_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_further_s5_sensitive_sensitivity analyse_dataset_adults_covid_s5_sensitive_sensitivity analyse_dataset_adults_covid_further_s5_sensitive_sensitivity process_dataset_adults_s6_sensitive_sensitivity describe_dataset_adults_s6_sensitive_sensitivity analyse_dataset_adults_rsv_s6_sensitive_sensitivity analyse_dataset_adults_flu_s6_sensitive_sensitivity analyse_dataset_adults_flu_further_s6_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_s6_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_further_s6_sensitive_sensitivity analyse_dataset_adults_covid_s6_sensitive_sensitivity analyse_dataset_adults_covid_further_s6_sensitive_sensitivity process_dataset_adults_s7_sensitive_sensitivity describe_dataset_adults_s7_sensitive_sensitivity analyse_dataset_adults_rsv_s7_sensitive_sensitivity analyse_dataset_adults_flu_s7_sensitive_sensitivity analyse_dataset_adults_flu_further_s7_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_s7_sensitive_sensitivity analyse_dataset_adults_overall_and_all_cause_further_s7_sensitive_sensitivity analyse_dataset_adults_covid_s7_sensitive_sensitivity analyse_dataset_adults_covid_further_s7_sensitive_sensitivity +process_dataset_children_and_adolescents_s1_sensitive_sensitivity describe_dataset_children_and_adolescents_s1_sensitive_sensitivity analyse_dataset_children_and_adolescents_rsv_s1_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_s1_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_further_s1_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_s1_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s1_sensitive_sensitivity process_dataset_children_and_adolescents_s2_sensitive_sensitivity describe_dataset_children_and_adolescents_s2_sensitive_sensitivity analyse_dataset_children_and_adolescents_rsv_s2_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_s2_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_further_s2_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_s2_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_sensitive_sensitivity process_dataset_children_and_adolescents_s3_sensitive_sensitivity describe_dataset_children_and_adolescents_s3_sensitive_sensitivity analyse_dataset_children_and_adolescents_rsv_s3_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_s3_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_further_s3_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_s3_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s3_sensitive_sensitivity process_dataset_children_and_adolescents_s4_sensitive_sensitivity describe_dataset_children_and_adolescents_s4_sensitive_sensitivity analyse_dataset_children_and_adolescents_rsv_s4_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_s4_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_further_s4_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_s4_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s4_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_s4_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_further_s4_sensitive_sensitivity process_dataset_children_and_adolescents_s5_sensitive_sensitivity describe_dataset_children_and_adolescents_s5_sensitive_sensitivity analyse_dataset_children_and_adolescents_rsv_s5_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_s5_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_further_s5_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_s5_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s5_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_s5_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_further_s5_sensitive_sensitivity process_dataset_children_and_adolescents_s6_sensitive_sensitivity describe_dataset_children_and_adolescents_s6_sensitive_sensitivity analyse_dataset_children_and_adolescents_rsv_s6_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_s6_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_further_s6_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_s6_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s6_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_s6_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_further_s6_sensitive_sensitivity process_dataset_children_and_adolescents_s7_sensitive_sensitivity describe_dataset_children_and_adolescents_s7_sensitive_sensitivity analyse_dataset_children_and_adolescents_rsv_s7_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_s7_sensitive_sensitivity analyse_dataset_children_and_adolescents_flu_further_s7_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_s7_sensitive_sensitivity analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s7_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_s7_sensitive_sensitivity analyse_dataset_children_and_adolescents_covid_further_s7_sensitive_sensitivity +process_dataset_infants_s1_sensitive_sensitivity describe_dataset_infants_s1_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_s1_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_s1_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_s1_sensitive_sensitivity analyse_dataset_infants_rsv_ses_s1_sensitive_sensitivity analyse_dataset_infants_flu_ses_s1_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_s1_sensitive_sensitivity analyse_dataset_infants_rsv_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_flu_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_ses_s1_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_ses_s1_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s1_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_rsv_ses_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_flu_ses_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s1_sensitive_sensitivity analyse_dataset_infants_rsv_full_s1_sensitive_sensitivity analyse_dataset_infants_flu_full_s1_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_full_s1_sensitive_sensitivity process_dataset_infants_s2_sensitive_sensitivity describe_dataset_infants_s2_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_s2_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_s2_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_s2_sensitive_sensitivity analyse_dataset_infants_rsv_ses_s2_sensitive_sensitivity analyse_dataset_infants_flu_ses_s2_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_s2_sensitive_sensitivity analyse_dataset_infants_rsv_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_flu_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_ses_s2_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_ses_s2_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s2_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_rsv_ses_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_flu_ses_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s2_sensitive_sensitivity analyse_dataset_infants_rsv_full_s2_sensitive_sensitivity analyse_dataset_infants_flu_full_s2_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_full_s2_sensitive_sensitivity process_dataset_infants_s3_sensitive_sensitivity describe_dataset_infants_s3_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_s3_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_s3_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_sensitivity analyse_dataset_infants_rsv_ses_s3_sensitive_sensitivity analyse_dataset_infants_flu_ses_s3_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_sensitivity analyse_dataset_infants_rsv_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_flu_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_ses_s3_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_ses_s3_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_rsv_ses_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_flu_ses_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_sensitive_sensitivity analyse_dataset_infants_rsv_full_s3_sensitive_sensitivity analyse_dataset_infants_flu_full_s3_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_full_s3_sensitive_sensitivity process_dataset_infants_s4_sensitive_sensitivity describe_dataset_infants_s4_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_s4_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_s4_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_sensitive_sensitivity analyse_dataset_infants_rsv_ses_s4_sensitive_sensitivity analyse_dataset_infants_flu_ses_s4_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_s4_sensitive_sensitivity analyse_dataset_infants_rsv_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_flu_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_ses_s4_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_ses_s4_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s4_sensitive_sensitivity analyse_dataset_infants_rsv_ethnicity_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_flu_ethnicity_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_rsv_ses_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_flu_ses_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_rsv_full_s4_sensitive_sensitivity analyse_dataset_infants_flu_full_s4_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_full_s4_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_s4_sensitive_sensitivity analyse_dataset_infants_covid_ses_s4_sensitive_sensitivity analyse_dataset_infants_covid_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_ses_s4_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_covid_ses_hh_comp_s4_sensitive_sensitivity analyse_dataset_infants_covid_full_s4_sensitive_sensitivity process_dataset_infants_s5_sensitive_sensitivity describe_dataset_infants_s5_sensitive_sensitivity 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analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_rsv_ses_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_flu_ses_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_rsv_full_s5_sensitive_sensitivity analyse_dataset_infants_flu_full_s5_sensitive_sensitivity analyse_dataset_infants_overall_and_all_cause_full_s5_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_s5_sensitive_sensitivity analyse_dataset_infants_covid_ses_s5_sensitive_sensitivity analyse_dataset_infants_covid_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_ses_s5_sensitive_sensitivity analyse_dataset_infants_covid_ethnicity_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_covid_ses_hh_comp_s5_sensitive_sensitivity analyse_dataset_infants_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_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 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_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 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_phenotype_sensitivity_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_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_phenotype_sensitivity_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_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_phenotype_sensitivity_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_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 630b477..ddee142 100644 --- a/create-project.R +++ b/create-project.R @@ -168,22 +168,22 @@ action_specified <- function(cohort, season, dates, codelist_type, action( name = glue("analyse_dataset_{cohort}_rsv_{season}_{codelist_type}_{investigation_type}"), run = glue("r:latest analysis/outcome_rsv/rsv_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), - arguments = c(cohort, season, dates, codelist_type, investigation_type, + arguments = c(cohort, season, dates, codelist_type, investigation_type, season_start_date, season_end_date), needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), moderately_sensitive = lst( csv = glue("output/results/models/rsv_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv")) ), - action( - name = glue("analyse_dataset_{cohort}_rsv_further_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/outcome_rsv/further_rsv_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), - arguments = c(cohort, season, dates, codelist_type, investigation_type, - season_start_date, season_end_date), - needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/rsv_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) - ), + # action( + # name = glue("analyse_dataset_{cohort}_rsv_further_{season}_{codelist_type}_{investigation_type}"), + # run = glue("r:latest analysis/outcome_rsv/further_rsv_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + # arguments = c(cohort, season, dates, codelist_type, investigation_type, + # season_start_date, season_end_date), + # needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/rsv_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) + # ), action( name = glue("analyse_dataset_{cohort}_flu_{season}_{codelist_type}_{investigation_type}"), @@ -208,23 +208,23 @@ action_specified <- function(cohort, season, dates, codelist_type, action( name = glue("analyse_dataset_{cohort}_overall_and_all_cause_{season}_{codelist_type}_{investigation_type}"), run = glue("r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), - arguments = c(cohort, season, dates, codelist_type, investigation_type, + arguments = c(cohort, season, dates, codelist_type, investigation_type, season_start_date, season_end_date), needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), moderately_sensitive = lst( csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv")) - ), - - action( - name = glue("analyse_dataset_{cohort}_overall_and_all_cause_further_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), - arguments = c(cohort, season, dates, codelist_type, investigation_type, - season_start_date, season_end_date), - needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) - - ) + )#, + + # action( + # name = glue("analyse_dataset_{cohort}_overall_and_all_cause_further_{season}_{codelist_type}_{investigation_type}"), + # run = glue("r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R {cohort} {season_start_date} {season_end_date} {codelist_type} {investigation_type}"), + # arguments = c(cohort, season, dates, codelist_type, investigation_type, + # season_start_date, season_end_date), + # needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/overall_and_all_cause_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")) + # + # ) ) @@ -481,217 +481,8 @@ action_specified_infants <- function(cohort, season, dates, codelist_type, needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_{investigation_type}")), moderately_sensitive = lst( csv = glue("output/results/models/overall_and_all_cause_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ses_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ses_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_ses_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_hh_comp_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_full_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_full_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_full_{season}_{codelist_type}_{investigation_type}"), - run = glue("r:latest analysis/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}_{codelist_type}_{investigation_type}")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_full_model_outputs_{cohort}_{dates}_{codelist_type}_{investigation_type}.csv")), ) + ) } @@ -801,76 +592,6 @@ action_covid_infants <- function(cohort, season, dates, codelist_type, 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")), ) ) @@ -918,15 +639,15 @@ action_secondary_rsv <- function(cohort, season, dates, codelist_type, 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}_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"), @@ -936,18 +657,18 @@ action_secondary_rsv <- function(cohort, season, dates, codelist_type, 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( + # 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")) + # + # ) ) @@ -1010,18 +731,18 @@ action_secondary_flu <- function(cohort, season, dates, codelist_type, 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( + # 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")) + # + # ) ) @@ -1083,17 +804,17 @@ action_secondary_covid <- function(cohort, season, dates, codelist_type, 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( + # 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")), + # ) ) @@ -1266,147 +987,147 @@ action_secondary_rsv_infants <- function(cohort, season, dates, codelist_type, 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( + # 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")), + # ) ) @@ -1579,147 +1300,147 @@ action_secondary_flu_infants <- function(cohort, season, dates, codelist_type, 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( + # 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")), + # ) ) @@ -1824,75 +1545,6 @@ action_secondary_covid_infants <- function(cohort, season, dates, codelist_type, csv = glue("output/results/models/covid_full_model_outputs_{cohort}_{dates}_specific_secondary.csv")), ), - action( - 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}_specific_secondary")), - moderately_sensitive = lst( - 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}_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}_specific_secondary")), - moderately_sensitive = lst( - 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}_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}_specific_secondary")), - moderately_sensitive = lst( - 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}_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}_specific_secondary")), - moderately_sensitive = lst( - 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}_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}_specific_secondary")), - moderately_sensitive = lst( - 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}_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}_specific_secondary")), - moderately_sensitive = lst( - 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}_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}_specific_secondary")), - moderately_sensitive = lst( - 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"), @@ -1962,77 +1614,147 @@ action_secondary_covid_infants <- function(cohort, season, dates, codelist_type, 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")), - ) + )#, + # + # action( + # 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}_specific_secondary")), + # moderately_sensitive = lst( + # 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}_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}_specific_secondary")), + # moderately_sensitive = lst( + # 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}_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}_specific_secondary")), + # moderately_sensitive = lst( + # 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}_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}_specific_secondary")), + # moderately_sensitive = lst( + # 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}_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}_specific_secondary")), + # moderately_sensitive = lst( + # 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}_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}_specific_secondary")), + # moderately_sensitive = lst( + # 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}_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}_specific_secondary")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_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")), + # ) ) @@ -2119,7 +1841,7 @@ action_sensitivity <- function(cohort, season, dates, season_start_date, needs = list(glue("generate_dataset_{cohort}_{season}_{codelist_type}_primary"), glue("process_household_information_{season}")), moderately_sensitive = lst( - csv = glue("output/sensitivity/input_processed_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + csv = glue("output/input_processed_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), ), action( @@ -2143,15 +1865,15 @@ action_sensitivity <- function(cohort, season, dates, season_start_date, csv = glue("output/results/models/rsv_{investigation_type}/*_{cohort}_{dates}_{codelist_type}_*.csv")), ), - action( - name = glue("analyse_dataset_{cohort}_rsv_further_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/rsv_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")), - ), + # action( + # name = glue("analyse_dataset_{cohort}_rsv_further_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/rsv_{investigation_type}/further_*_{cohort}_{dates}_{codelist_type}_*.csv")), + # ), action( name = glue("analyse_dataset_{cohort}_flu_{season}_{codelist_type}_sensitivity"), @@ -2211,7 +1933,7 @@ action_sensitivity_infants <- function(cohort, season, dates, season_start_date, needs = list(glue("generate_dataset_{cohort}_{season}_{codelist_type}_primary"), glue("process_household_information_{season}")), moderately_sensitive = lst( - csv = glue("output/sensitivity/input_processed_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + csv = glue("output/input_processed_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), ), action( @@ -2433,217 +2155,217 @@ action_sensitivity_infants <- function(cohort, season, dates, season_start_date, needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_sensitivity")), moderately_sensitive = lst( csv = glue("output/results/models/overall_and_all_cause_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ses_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ses_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_ses_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_ses_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_ses_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_ses_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_ses_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_rsv_full_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_rsv_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_flu_full_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_flu_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_full_{season}_{codelist_type}_sensitivity"), - 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}_{codelist_type}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_overall_and_all_cause_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ) + )#, + # + # action( + # name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_rsv_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_flu_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_rsv_ses_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_rsv_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_flu_ses_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_flu_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_overall_and_all_cause_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_rsv_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_rsv_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_flu_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_flu_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_ses_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_rsv_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_ses_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_flu_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_ses_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_rsv_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_flu_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_flu_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_rsv_ses_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_rsv_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_flu_ses_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_flu_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_ses_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_rsv_full_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_rsv_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_flu_full_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_flu_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_overall_and_all_cause_full_{season}_{codelist_type}_sensitivity"), + # 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}_{codelist_type}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_overall_and_all_cause_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ) ) @@ -2753,77 +2475,77 @@ action_covid_sensitivity_infants <- function(cohort, season, dates, needs = list(glue("process_dataset_{cohort}_{season}_{codelist_type}_sensitivity")), moderately_sensitive = lst( csv = glue("output/results/models/covid_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_{season}_{codelist_type}_sensitivity"), - 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}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}further__covid_ses_{season}_{codelist_type}_sensitivity"), - 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}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_covid_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_ses_{season}_{codelist_type}_sensitivity"), - 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}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_covid_ses_hh_comp_{season}_{codelist_type}_sensitivity"), - 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}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ), - - action( - name = glue("analyse_dataset_{cohort}_further_covid_full_{season}_{codelist_type}_sensitivity"), - 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}_sensitivity")), - moderately_sensitive = lst( - csv = glue("output/results/models/further_covid_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), - ) + )#, + # + # action( + # name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_{season}_{codelist_type}_sensitivity"), + # 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}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_ethnicity_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}further__covid_ses_{season}_{codelist_type}_sensitivity"), + # 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}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_covid_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_ses_{season}_{codelist_type}_sensitivity"), + # 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}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_ethnicity_ses_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_covid_ethnicity_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_ethnicity_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_covid_ses_hh_comp_{season}_{codelist_type}_sensitivity"), + # 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}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_ses_hh_comp_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ), + # + # action( + # name = glue("analyse_dataset_{cohort}_further_covid_full_{season}_{codelist_type}_sensitivity"), + # 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}_sensitivity")), + # moderately_sensitive = lst( + # csv = glue("output/results/models/further_covid_full_model_outputs_{cohort}_{dates}_{codelist_type}_sensitivity.csv")), + # ) ) diff --git a/project.yaml b/project.yaml index 7f550d6..6e8a830 100644 --- a/project.yaml +++ b/project.yaml @@ -749,16 +749,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2016_2017_specific_*.csv - analyse_dataset_older_adults_rsv_further_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season1_start_date - season1_end_date specific primary older_adults s1 2016_2017 specific primary - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2016_2017_specific_*.csv - analyse_dataset_older_adults_flu_s1_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season1_start_date season1_end_date specific primary older_adults s1 2016_2017 specific primary @@ -789,16 +779,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2016_2017_specific_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season1_start_date season1_end_date specific primary older_adults - s1 2016_2017 specific primary season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2016_2017_specific_*.csv - generate_dataset_older_adults_s2_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -840,16 +820,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2017_2018_specific_*.csv - analyse_dataset_older_adults_rsv_further_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season2_start_date - season2_end_date specific primary older_adults s2 2017_2018 specific primary - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2017_2018_specific_*.csv - analyse_dataset_older_adults_flu_s2_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season2_start_date season2_end_date specific primary older_adults s2 2017_2018 specific primary @@ -880,16 +850,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2017_2018_specific_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season2_start_date season2_end_date specific primary older_adults - s2 2017_2018 specific primary season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2017_2018_specific_*.csv - generate_dataset_older_adults_s3_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -931,16 +891,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2018_2019_specific_*.csv - analyse_dataset_older_adults_rsv_further_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season3_start_date - season3_end_date specific primary older_adults s3 2018_2019 specific primary - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2018_2019_specific_*.csv - analyse_dataset_older_adults_flu_s3_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season3_start_date season3_end_date specific primary older_adults s3 2018_2019 specific primary @@ -971,16 +921,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2018_2019_specific_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season3_start_date season3_end_date specific primary older_adults - s3 2018_2019 specific primary season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2018_2019_specific_*.csv - generate_dataset_older_adults_s4_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -1022,16 +962,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2019_2020_specific_*.csv - analyse_dataset_older_adults_rsv_further_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season4_start_date - season4_end_date specific primary older_adults s4 2019_2020 specific primary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2019_2020_specific_*.csv - analyse_dataset_older_adults_flu_s4_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season4_start_date season4_end_date specific primary older_adults s4 2019_2020 specific primary @@ -1062,16 +992,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2019_2020_specific_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season4_start_date season4_end_date specific primary older_adults - s4 2019_2020 specific primary season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2019_2020_specific_*.csv - analyse_dataset_older_adults_covid_s4_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season4_start_date season4_end_date specific primary older_adults s4 2019_2020 specific primary @@ -1133,16 +1053,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2020_2021_specific_*.csv - analyse_dataset_older_adults_rsv_further_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season5_start_date - season5_end_date specific primary older_adults s5 2020_2021 specific primary - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2020_2021_specific_*.csv - analyse_dataset_older_adults_flu_s5_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season5_start_date season5_end_date specific primary older_adults s5 2020_2021 specific primary @@ -1173,16 +1083,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2020_2021_specific_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season5_start_date season5_end_date specific primary older_adults - s5 2020_2021 specific primary season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2020_2021_specific_*.csv - analyse_dataset_older_adults_covid_s5_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season5_start_date season5_end_date specific primary older_adults s5 2020_2021 specific primary @@ -1244,16 +1144,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2021_2022_specific_*.csv - analyse_dataset_older_adults_rsv_further_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season6_start_date - season6_end_date specific primary older_adults s6 2021_2022 specific primary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2021_2022_specific_*.csv - analyse_dataset_older_adults_flu_s6_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season6_start_date season6_end_date specific primary older_adults s6 2021_2022 specific primary @@ -1284,16 +1174,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2021_2022_specific_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season6_start_date season6_end_date specific primary older_adults - s6 2021_2022 specific primary season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2021_2022_specific_*.csv - analyse_dataset_older_adults_covid_s6_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season6_start_date season6_end_date specific primary older_adults s6 2021_2022 specific primary @@ -1355,16 +1235,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2022_2023_specific_*.csv - analyse_dataset_older_adults_rsv_further_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season7_start_date - season7_end_date specific primary older_adults s7 2022_2023 specific primary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2022_2023_specific_*.csv - analyse_dataset_older_adults_flu_s7_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season7_start_date season7_end_date specific primary older_adults s7 2022_2023 specific primary @@ -1395,16 +1265,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2022_2023_specific_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season7_start_date season7_end_date specific primary older_adults - s7 2022_2023 specific primary season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2022_2023_specific_*.csv - analyse_dataset_older_adults_covid_s7_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season7_start_date season7_end_date specific primary older_adults s7 2022_2023 specific primary @@ -1470,16 +1330,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2016_2017_specific_*.csv - analyse_dataset_adults_rsv_further_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season1_start_date - season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_adults_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2016_2017_specific_*.csv - analyse_dataset_adults_flu_s1_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season1_start_date season1_end_date specific primary adults s1 2016_2017 specific primary season1_start_date @@ -1510,16 +1360,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2016_2017_specific_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season1_start_date season1_end_date specific primary adults s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_adults_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2016_2017_specific_*.csv - generate_dataset_adults_s2_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -1559,16 +1399,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2017_2018_specific_*.csv - analyse_dataset_adults_rsv_further_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season2_start_date - season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date - season2_end_date - needs: - - process_dataset_adults_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2017_2018_specific_*.csv - analyse_dataset_adults_flu_s2_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season2_start_date season2_end_date specific primary adults s2 2017_2018 specific primary season2_start_date @@ -1599,16 +1429,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2017_2018_specific_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season2_start_date season2_end_date specific primary adults s2 2017_2018 - specific primary season2_start_date season2_end_date - needs: - - process_dataset_adults_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2017_2018_specific_*.csv - generate_dataset_adults_s3_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -1648,16 +1468,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2018_2019_specific_*.csv - analyse_dataset_adults_rsv_further_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season3_start_date - season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_adults_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2018_2019_specific_*.csv - analyse_dataset_adults_flu_s3_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season3_start_date season3_end_date specific primary adults s3 2018_2019 specific primary season3_start_date @@ -1688,16 +1498,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2018_2019_specific_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season3_start_date season3_end_date specific primary adults s3 2018_2019 - specific primary season3_start_date season3_end_date - needs: - - process_dataset_adults_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2018_2019_specific_*.csv - generate_dataset_adults_s4_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -1737,16 +1537,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2019_2020_specific_*.csv - analyse_dataset_adults_rsv_further_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season4_start_date - season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_adults_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2019_2020_specific_*.csv - analyse_dataset_adults_flu_s4_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season4_start_date season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date @@ -1777,16 +1567,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2019_2020_specific_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season4_start_date season4_end_date specific primary adults s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_adults_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2019_2020_specific_*.csv - analyse_dataset_adults_covid_s4_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season4_start_date season4_end_date specific primary adults s4 2019_2020 specific primary season4_start_date @@ -1846,16 +1626,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2020_2021_specific_*.csv - analyse_dataset_adults_rsv_further_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season5_start_date - season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_adults_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2020_2021_specific_*.csv - analyse_dataset_adults_flu_s5_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season5_start_date season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date @@ -1886,16 +1656,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2020_2021_specific_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season5_start_date season5_end_date specific primary adults s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_adults_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2020_2021_specific_*.csv - analyse_dataset_adults_covid_s5_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season5_start_date season5_end_date specific primary adults s5 2020_2021 specific primary season5_start_date @@ -1955,16 +1715,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2021_2022_specific_*.csv - analyse_dataset_adults_rsv_further_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season6_start_date - season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_adults_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2021_2022_specific_*.csv - analyse_dataset_adults_flu_s6_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season6_start_date season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date @@ -1995,16 +1745,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2021_2022_specific_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season6_start_date season6_end_date specific primary adults s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_adults_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2021_2022_specific_*.csv - analyse_dataset_adults_covid_s6_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season6_start_date season6_end_date specific primary adults s6 2021_2022 specific primary season6_start_date @@ -2064,16 +1804,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2022_2023_specific_*.csv - analyse_dataset_adults_rsv_further_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season7_start_date - season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_adults_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2022_2023_specific_*.csv - analyse_dataset_adults_flu_s7_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season7_start_date season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date @@ -2104,16 +1834,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2022_2023_specific_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season7_start_date season7_end_date specific primary adults s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_adults_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2022_2023_specific_*.csv - analyse_dataset_adults_covid_s7_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season7_start_date season7_end_date specific primary adults s7 2022_2023 specific primary season7_start_date @@ -2180,16 +1900,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2016_2017_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season1_start_date season1_end_date specific primary children_and_adolescents - s1 2016_2017 specific primary season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2016_2017_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s1_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season1_start_date season1_end_date specific primary children_and_adolescents @@ -2220,16 +1930,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2016_2017_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season1_start_date season1_end_date specific primary - children_and_adolescents s1 2016_2017 specific primary season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2016_2017_specific_*.csv - generate_dataset_children_and_adolescents_s2_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -2271,16 +1971,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season2_start_date season2_end_date specific primary children_and_adolescents - s2 2017_2018 specific primary season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s2_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season2_start_date season2_end_date specific primary children_and_adolescents @@ -2311,16 +2001,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season2_start_date season2_end_date specific primary - children_and_adolescents s2 2017_2018 specific primary season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2017_2018_specific_*.csv - generate_dataset_children_and_adolescents_s3_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -2362,16 +2042,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season3_start_date season3_end_date specific primary children_and_adolescents - s3 2018_2019 specific primary season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s3_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season3_start_date season3_end_date specific primary children_and_adolescents @@ -2402,16 +2072,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season3_start_date season3_end_date specific primary - children_and_adolescents s3 2018_2019 specific primary season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2018_2019_specific_*.csv - generate_dataset_children_and_adolescents_s4_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -2453,16 +2113,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2019_2020_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season4_start_date season4_end_date specific primary children_and_adolescents - s4 2019_2020 specific primary season4_start_date season4_end_date - needs: - - process_dataset_children_and_adolescents_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2019_2020_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s4_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season4_start_date season4_end_date specific primary children_and_adolescents @@ -2493,16 +2143,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2019_2020_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season4_start_date season4_end_date specific primary - children_and_adolescents s4 2019_2020 specific primary season4_start_date season4_end_date - needs: - - process_dataset_children_and_adolescents_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2019_2020_specific_*.csv - analyse_dataset_children_and_adolescents_covid_s4_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season4_start_date season4_end_date specific primary children_and_adolescents @@ -2564,25 +2204,15 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2020_2021_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents + analyse_dataset_children_and_adolescents_flu_s5_specific_primary: + run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season5_start_date season5_end_date specific primary children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date needs: - process_dataset_children_and_adolescents_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2020_2021_specific_*.csv - - analyse_dataset_children_and_adolescents_flu_s5_specific_primary: - run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents - season5_start_date season5_end_date specific primary children_and_adolescents - s5 2020_2021 specific primary season5_start_date season5_end_date - needs: - - process_dataset_children_and_adolescents_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_primary/*_children_and_adolescents_2020_2021_specific_*.csv + csv: output/results/models/flu_primary/*_children_and_adolescents_2020_2021_specific_*.csv analyse_dataset_children_and_adolescents_flu_further_s5_specific_primary: run: r:latest analysis/outcome_flu/further_flu_models_master.R children_and_adolescents @@ -2604,16 +2234,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2020_2021_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season5_start_date season5_end_date specific primary - children_and_adolescents s5 2020_2021 specific primary season5_start_date season5_end_date - needs: - - process_dataset_children_and_adolescents_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2020_2021_specific_*.csv - analyse_dataset_children_and_adolescents_covid_s5_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season5_start_date season5_end_date specific primary children_and_adolescents @@ -2675,16 +2295,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2021_2022_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season6_start_date season6_end_date specific primary children_and_adolescents - s6 2021_2022 specific primary season6_start_date season6_end_date - needs: - - process_dataset_children_and_adolescents_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2021_2022_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s6_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season6_start_date season6_end_date specific primary children_and_adolescents @@ -2715,16 +2325,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2021_2022_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season6_start_date season6_end_date specific primary - children_and_adolescents s6 2021_2022 specific primary season6_start_date season6_end_date - needs: - - process_dataset_children_and_adolescents_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2021_2022_specific_*.csv - analyse_dataset_children_and_adolescents_covid_s6_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season6_start_date season6_end_date specific primary children_and_adolescents @@ -2786,16 +2386,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2022_2023_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season7_start_date season7_end_date specific primary children_and_adolescents - s7 2022_2023 specific primary season7_start_date season7_end_date - needs: - - process_dataset_children_and_adolescents_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2022_2023_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s7_specific_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season7_start_date season7_end_date specific primary children_and_adolescents @@ -2826,16 +2416,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2022_2023_specific_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season7_start_date season7_end_date specific primary - children_and_adolescents s7 2022_2023 specific primary season7_start_date season7_end_date - needs: - - process_dataset_children_and_adolescents_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2022_2023_specific_*.csv - analyse_dataset_children_and_adolescents_covid_s7_specific_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season7_start_date season7_end_date specific primary children_and_adolescents @@ -3099,216 +2679,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2016_2017_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_s1_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season1_start_date season1_end_date specific primary infants s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_s1_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season1_start_date season1_end_date specific primary infants s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_rsv_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_flu_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season1_start_date season1_end_date specific primary infants s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season1_start_date season1_end_date specific primary infants s1 2016_2017 specific - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s1_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season1_start_date season1_end_date specific primary infants s1 2016_2017 specific - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season1_start_date season1_end_date specific primary infants s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date specific primary infants s1 2016_2017 specific - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date specific primary infants s1 2016_2017 specific - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season1_start_date season1_end_date specific primary infants s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season1_start_date season1_end_date specific primary infants s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_rsv_full_s1_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_flu_full_s1_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season1_start_date - season1_end_date specific primary infants s1 2016_2017 specific primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2016_2017_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s1_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season1_start_date season1_end_date specific primary infants s1 2016_2017 - specific primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2016_2017_specific_primary.csv - generate_dataset_infants_s2_specific_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -3548,284 +2918,74 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_specific_primary + generate_dataset_infants_s3_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2018_2019_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow + -- infants season3_start_date season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date season3_end_date outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + highly_sensitive: + dataset: output/data/input_infants_2018_2019_specific_primary.arrow - analyse_dataset_infants_further_flu_ethnicity_s2_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date + process_dataset_infants_s3_specific_primary: + run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date + specific primary infants s3 2018_2019 specific primary season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_primary + - generate_dataset_infants_s3_specific_primary + - process_household_information_s3 outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + highly_sensitive: + cohort: output/data/input_processed_infants_2018_2019_specific_primary.arrow - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_specific_primary: - 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 primary infants s2 2017_2018 - specific primary season2_start_date season2_end_date + describe_dataset_infants_s3_specific_primary: + run: r:latest analysis/report.R infants season3_start_date season3_end_date specific + primary infants s3 2018_2019 specific primary season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_primary + - process_dataset_infants_s3_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_specific_primary.csv + csv: output/results/rates/rates_infants_2018_2019_specific_primary.csv - analyse_dataset_infants_further_rsv_ses_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date + analyse_dataset_infants_rsv_ethnicity_s3_specific_primary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_specific_primary + - process_dataset_infants_s3_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_specific_primary.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv - analyse_dataset_infants_further_flu_ses_s2_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date + analyse_dataset_infants_flu_ethnicity_s3_specific_primary: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_specific_primary + - process_dataset_infants_s3_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2017_2018_specific_primary.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s2_specific_primary: - 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 primary infants s2 2017_2018 - specific primary season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_specific_primary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date specific primary infants s3 2018_2019 + specific primary season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_primary + - process_dataset_infants_s3_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_specific_primary.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date + analyse_dataset_infants_rsv_ses_s3_specific_primary: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date + season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_specific_primary + - process_dataset_infants_s3_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_flu_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season2_start_date season2_end_date specific primary infants s2 2017_2018 - specific primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season2_start_date season2_end_date specific primary infants s2 2017_2018 specific - primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s2_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season2_start_date season2_end_date specific primary infants s2 2017_2018 specific - primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season2_start_date season2_end_date specific primary infants s2 2017_2018 - specific primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date specific primary infants s2 2017_2018 specific - primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date specific primary infants s2 2017_2018 specific - primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season2_start_date season2_end_date specific primary infants s2 2017_2018 - specific primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season2_start_date season2_end_date specific primary infants s2 2017_2018 - specific primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_rsv_full_s2_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_flu_full_s2_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season2_start_date - season2_end_date specific primary infants s2 2017_2018 specific primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2017_2018_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s2_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season2_start_date season2_end_date specific primary infants s2 2017_2018 - specific primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_primary.csv - - generate_dataset_infants_s3_specific_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2018_2019_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow - -- infants season3_start_date season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date season3_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2018_2019_specific_primary.arrow - - process_dataset_infants_s3_specific_primary: - run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date - specific primary infants s3 2018_2019 specific primary season3_start_date season3_end_date - needs: - - generate_dataset_infants_s3_specific_primary - - process_household_information_s3 - outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2018_2019_specific_primary.arrow - - describe_dataset_infants_s3_specific_primary: - run: r:latest analysis/report.R infants season3_start_date season3_end_date specific - primary infants s3 2018_2019 specific primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_rsv_ethnicity_s3_specific_primary: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_flu_ethnicity_s3_specific_primary: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season3_start_date season3_end_date specific primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_rsv_ses_s3_specific_primary: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_specific_primary.csv analyse_dataset_infants_flu_ses_s3_specific_primary: run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date @@ -3997,314 +3157,104 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary + generate_dataset_infants_s4_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2019_2020_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow + -- infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + highly_sensitive: + dataset: output/data/input_infants_2019_2020_specific_primary.arrow - analyse_dataset_infants_further_flu_ethnicity_s3_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date + process_dataset_infants_s4_specific_primary: + run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date + specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - generate_dataset_infants_s4_specific_primary + - process_household_information_s4 outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + highly_sensitive: + cohort: output/data/input_processed_infants_2019_2020_specific_primary.arrow - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_specific_primary: - 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 primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date + describe_dataset_infants_s4_specific_primary: + run: r:latest analysis/report.R infants season4_start_date season4_end_date specific + primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/rates/rates_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_rsv_ses_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date + analyse_dataset_infants_rsv_ethnicity_s4_specific_primary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_flu_ses_s3_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date + analyse_dataset_infants_flu_ethnicity_s4_specific_primary: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s3_specific_primary: - 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 primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_specific_primary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date + analyse_dataset_infants_rsv_ses_s4_specific_primary: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date + analyse_dataset_infants_flu_ses_s4_specific_primary: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_specific_primary: - 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 primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date + analyse_dataset_infants_overall_and_all_cause_ses_s4_specific_primary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date specific primary infants s4 2019_2020 + specific primary season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_ses_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season3_start_date season3_end_date specific primary infants s3 2018_2019 specific - primary season3_start_date season3_end_date + analyse_dataset_infants_rsv_hh_comp_s4_specific_primary: + run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season4_start_date + season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_specific_primary + - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s3_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season3_start_date season3_end_date specific primary infants s3 2018_2019 specific - primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season3_start_date season3_end_date specific primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date specific primary infants s3 2018_2019 specific - primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date specific primary infants s3 2018_2019 specific - primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season3_start_date season3_end_date specific primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season3_start_date season3_end_date specific primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_rsv_full_s3_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_flu_full_s3_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season3_start_date - season3_end_date specific primary infants s3 2018_2019 specific primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s3_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season3_start_date season3_end_date specific primary infants s3 2018_2019 - specific primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_primary.csv - - generate_dataset_infants_s4_specific_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2019_2020_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow - -- infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2019_2020_specific_primary.arrow - - process_dataset_infants_s4_specific_primary: - run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date - specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date - needs: - - generate_dataset_infants_s4_specific_primary - - process_household_information_s4 - outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2019_2020_specific_primary.arrow - - describe_dataset_infants_s4_specific_primary: - run: r:latest analysis/report.R infants season4_start_date season4_end_date specific - primary infants s4 2019_2020 specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_rsv_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_flu_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_rsv_ses_s4_specific_primary: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_flu_ses_s4_specific_primary: - run: r:latest analysis/outcome_flu/flu_ses_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_overall_and_all_cause_ses_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_rsv_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv analyse_dataset_infants_flu_hh_comp_s4_specific_primary: run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season4_start_date @@ -4446,404 +3396,124 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season4_start_date + analyse_dataset_infants_covid_ethnicity_s4_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season4_start_date + analyse_dataset_infants_covid_ses_s4_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_rsv_ses_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season4_start_date + analyse_dataset_infants_covid_hh_comp_s4_specific_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_flu_ses_s4_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season4_start_date + analyse_dataset_infants_covid_ethnicity_ses_s4_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s4_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date specific primary infants s4 2019_2020 specific + primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_covid_ses_hh_comp_s4_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_covid_full_s4_specific_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season4_start_date season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2019_2020_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary + generate_dataset_infants_s5_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2020_2021_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow + -- infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv + highly_sensitive: + dataset: output/data/input_infants_2020_2021_specific_primary.arrow - analyse_dataset_infants_further_rsv_ethnicity_ses_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date + process_dataset_infants_s5_specific_primary: + run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date + specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_primary + - generate_dataset_infants_s5_specific_primary + - process_household_information_s5 outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + highly_sensitive: + cohort: output/data/input_processed_infants_2020_2021_specific_primary.arrow - analyse_dataset_infants_further_flu_ethnicity_ses_s4_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date + describe_dataset_infants_s5_specific_primary: + run: r:latest analysis/report.R infants season5_start_date season5_end_date specific + primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_primary + - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/rates/rates_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date + analyse_dataset_infants_rsv_ethnicity_s5_specific_primary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date needs: - - process_dataset_infants_s4_specific_primary + - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date + analyse_dataset_infants_flu_ethnicity_s5_specific_primary: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season5_start_date + season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date + season5_end_date needs: - - process_dataset_infants_s4_specific_primary + - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_rsv_full_s4_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_flu_full_s4_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s4_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_covid_ses_s4_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_covid_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s4_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_covid_full_s4_specific_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s4_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s4_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s4_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date specific primary infants s4 2019_2020 - specific primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s4_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season4_start_date season4_end_date specific primary infants s4 2019_2020 specific - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_primary.csv - - analyse_dataset_infants_further_covid_full_s4_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season4_start_date - season4_end_date specific primary infants s4 2019_2020 specific primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2019_2020_specific_primary.csv - - generate_dataset_infants_s5_specific_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2020_2021_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow - -- infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2020_2021_specific_primary.arrow - - process_dataset_infants_s5_specific_primary: - run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date - specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date - needs: - - generate_dataset_infants_s5_specific_primary - - process_household_information_s5 - outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2020_2021_specific_primary.arrow - - describe_dataset_infants_s5_specific_primary: - run: r:latest analysis/report.R infants season5_start_date season5_end_date specific - primary infants s5 2020_2021 specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_rsv_ethnicity_s5_specific_primary: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_flu_ethnicity_s5_specific_primary: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_primary: run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R @@ -5035,355 +3705,75 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season5_start_date + analyse_dataset_infants_covid_ethnicity_s5_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s5_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season5_start_date + analyse_dataset_infants_covid_ses_s5_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_rsv_ses_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season5_start_date + analyse_dataset_infants_covid_hh_comp_s5_specific_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_flu_ses_s5_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season5_start_date + analyse_dataset_infants_covid_ethnicity_ses_s5_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date specific primary infants s5 2020_2021 specific + primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season5_start_date + analyse_dataset_infants_covid_ses_hh_comp_s5_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season5_start_date + analyse_dataset_infants_covid_full_s5_specific_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season5_start_date season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s5_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_rsv_full_s5_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_flu_full_s5_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s5_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_s5_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_covid_ses_s5_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_covid_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s5_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_covid_full_s5_specific_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s5_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s5_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s5_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season5_start_date season5_end_date specific primary infants s5 2020_2021 - specific primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s5_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season5_start_date season5_end_date specific primary infants s5 2020_2021 specific - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_primary.csv - - analyse_dataset_infants_further_covid_full_s5_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season5_start_date - season5_end_date specific primary infants s5 2020_2021 specific primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_specific_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2020_2021_specific_primary.csv generate_dataset_infants_s6_specific_primary: run: |- @@ -5624,365 +4014,85 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season6_start_date + analyse_dataset_infants_covid_ethnicity_s6_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season6_start_date season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s6_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season6_start_date + analyse_dataset_infants_covid_ses_s6_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season6_start_date season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_rsv_ses_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season6_start_date + analyse_dataset_infants_covid_hh_comp_s6_specific_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season6_start_date season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2021_2022_specific_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_flu_ses_s6_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season6_start_date + analyse_dataset_infants_covid_ethnicity_ses_s6_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season6_start_date season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2021_2022_specific_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s6_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date specific primary infants s6 2021_2022 specific + primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2021_2022_specific_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season6_start_date + analyse_dataset_infants_covid_ses_hh_comp_s6_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season6_start_date season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season6_start_date + analyse_dataset_infants_covid_full_s6_specific_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season6_start_date season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2021_2022_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary + generate_dataset_infants_s7_specific_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2022_2023_specific_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow + -- infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s6_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_rsv_full_s6_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_flu_full_s6_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s6_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_s6_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_covid_ses_s6_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_covid_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s6_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_covid_full_s6_specific_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s6_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s6_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s6_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date specific primary infants s6 2021_2022 - specific primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s6_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season6_start_date season6_end_date specific primary infants s6 2021_2022 specific - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_primary.csv - - analyse_dataset_infants_further_covid_full_s6_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season6_start_date - season6_end_date specific primary infants s6 2021_2022 specific primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2021_2022_specific_primary.csv - - generate_dataset_infants_s7_specific_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2022_2023_specific_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow - -- infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2022_2023_specific_primary.arrow + highly_sensitive: + dataset: output/data/input_infants_2022_2023_specific_primary.arrow process_dataset_infants_s7_specific_primary: run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date @@ -6213,361 +4323,81 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season7_start_date + analyse_dataset_infants_covid_ethnicity_s7_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s7_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season7_start_date + analyse_dataset_infants_covid_ses_s7_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_rsv_ses_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season7_start_date + analyse_dataset_infants_covid_hh_comp_s7_specific_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2022_2023_specific_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_flu_ses_s7_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season7_start_date + analyse_dataset_infants_covid_ethnicity_ses_s7_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2022_2023_specific_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s7_specific_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date specific primary infants s7 2022_2023 specific + primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2022_2023_specific_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season7_start_date + analyse_dataset_infants_covid_ses_hh_comp_s7_specific_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season7_start_date + analyse_dataset_infants_covid_full_s7_specific_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season7_start_date season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2022_2023_specific_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s7_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_rsv_full_s7_specific_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_flu_full_s7_specific_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s7_specific_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_s7_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_covid_ses_s7_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_covid_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s7_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_covid_full_s7_specific_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s7_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s7_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s7_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date specific primary infants s7 2022_2023 - specific primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s7_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season7_start_date season7_end_date specific primary infants s7 2022_2023 specific - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_primary.csv - - analyse_dataset_infants_further_covid_full_s7_specific_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season7_start_date - season7_end_date specific primary infants s7 2022_2023 specific primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_specific_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2022_2023_specific_primary.csv - - ## # # # # # # # # # # # # # # # # # # # - ## SENSITIVE PHENOTYPES - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Older Adults, Codelist Type: Sensitive, Investigation Type: Primary + ## # # # # # # # # # # # # # # # # # # # + ## SENSITIVE PHENOTYPES + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults, Codelist Type: Sensitive, Investigation Type: Primary ## # # # # # # # # # # # # # # # # # # # @@ -6613,16 +4443,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2016_2017_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season1_start_date - season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2016_2017_sensitive_*.csv - analyse_dataset_older_adults_flu_s1_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season1_start_date season1_end_date sensitive primary older_adults s1 2016_2017 sensitive primary @@ -6653,16 +4473,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2016_2017_sensitive_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season1_start_date season1_end_date sensitive primary older_adults - s1 2016_2017 sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2016_2017_sensitive_*.csv - generate_dataset_older_adults_s2_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -6704,16 +4514,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2017_2018_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season2_start_date - season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2017_2018_sensitive_*.csv - analyse_dataset_older_adults_flu_s2_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season2_start_date season2_end_date sensitive primary older_adults s2 2017_2018 sensitive primary @@ -6744,16 +4544,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2017_2018_sensitive_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season2_start_date season2_end_date sensitive primary older_adults - s2 2017_2018 sensitive primary season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2017_2018_sensitive_*.csv - generate_dataset_older_adults_s3_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -6795,16 +4585,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2018_2019_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season3_start_date - season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2018_2019_sensitive_*.csv - analyse_dataset_older_adults_flu_s3_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season3_start_date season3_end_date sensitive primary older_adults s3 2018_2019 sensitive primary @@ -6835,16 +4615,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2018_2019_sensitive_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season3_start_date season3_end_date sensitive primary older_adults - s3 2018_2019 sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2018_2019_sensitive_*.csv - generate_dataset_older_adults_s4_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -6886,16 +4656,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2019_2020_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season4_start_date - season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2019_2020_sensitive_*.csv - analyse_dataset_older_adults_flu_s4_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary @@ -6926,16 +4686,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2019_2020_sensitive_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season4_start_date season4_end_date sensitive primary older_adults - s4 2019_2020 sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2019_2020_sensitive_*.csv - analyse_dataset_older_adults_covid_s4_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season4_start_date season4_end_date sensitive primary older_adults s4 2019_2020 sensitive primary @@ -6997,16 +4747,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2020_2021_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season5_start_date - season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2020_2021_sensitive_*.csv - analyse_dataset_older_adults_flu_s5_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary @@ -7037,16 +4777,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2020_2021_sensitive_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season5_start_date season5_end_date sensitive primary older_adults - s5 2020_2021 sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2020_2021_sensitive_*.csv - analyse_dataset_older_adults_covid_s5_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season5_start_date season5_end_date sensitive primary older_adults s5 2020_2021 sensitive primary @@ -7108,16 +4838,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2021_2022_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season6_start_date - season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2021_2022_sensitive_*.csv - analyse_dataset_older_adults_flu_s6_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary @@ -7148,16 +4868,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2021_2022_sensitive_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season6_start_date season6_end_date sensitive primary older_adults - s6 2021_2022 sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2021_2022_sensitive_*.csv - analyse_dataset_older_adults_covid_s6_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season6_start_date season6_end_date sensitive primary older_adults s6 2021_2022 sensitive primary @@ -7219,16 +4929,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_older_adults_2022_2023_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R older_adults season7_start_date - season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_older_adults_2022_2023_sensitive_*.csv - analyse_dataset_older_adults_flu_s7_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R older_adults season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary @@ -7259,16 +4959,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_older_adults_2022_2023_sensitive_*.csv - analyse_dataset_older_adults_overall_and_all_cause_further_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - older_adults season7_start_date season7_end_date sensitive primary older_adults - s7 2022_2023 sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_older_adults_2022_2023_sensitive_*.csv - analyse_dataset_older_adults_covid_s7_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R older_adults season7_start_date season7_end_date sensitive primary older_adults s7 2022_2023 sensitive primary @@ -7332,16 +5022,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2016_2017_sensitive_*.csv - analyse_dataset_adults_rsv_further_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season1_start_date - season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_adults_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2016_2017_sensitive_*.csv - analyse_dataset_adults_flu_s1_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 sensitive primary season1_start_date @@ -7372,16 +5052,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2016_2017_sensitive_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season1_start_date season1_end_date sensitive primary adults s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_adults_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2016_2017_sensitive_*.csv - generate_dataset_adults_s2_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -7421,16 +5091,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2017_2018_sensitive_*.csv - analyse_dataset_adults_rsv_further_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season2_start_date - season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date - season2_end_date - needs: - - process_dataset_adults_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2017_2018_sensitive_*.csv - analyse_dataset_adults_flu_s2_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 sensitive primary season2_start_date @@ -7461,16 +5121,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2017_2018_sensitive_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season2_start_date season2_end_date sensitive primary adults s2 2017_2018 - sensitive primary season2_start_date season2_end_date - needs: - - process_dataset_adults_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2017_2018_sensitive_*.csv - generate_dataset_adults_s3_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -7510,16 +5160,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2018_2019_sensitive_*.csv - analyse_dataset_adults_rsv_further_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season3_start_date - season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_adults_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2018_2019_sensitive_*.csv - analyse_dataset_adults_flu_s3_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 sensitive primary season3_start_date @@ -7550,16 +5190,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2018_2019_sensitive_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season3_start_date season3_end_date sensitive primary adults s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_adults_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2018_2019_sensitive_*.csv - generate_dataset_adults_s4_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -7599,16 +5229,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2019_2020_sensitive_*.csv - analyse_dataset_adults_rsv_further_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season4_start_date - season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_adults_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2019_2020_sensitive_*.csv - analyse_dataset_adults_flu_s4_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date @@ -7639,16 +5259,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2019_2020_sensitive_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_adults_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2019_2020_sensitive_*.csv - analyse_dataset_adults_covid_s4_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season4_start_date season4_end_date sensitive primary adults s4 2019_2020 sensitive primary season4_start_date @@ -7708,16 +5318,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2020_2021_sensitive_*.csv - analyse_dataset_adults_rsv_further_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season5_start_date - season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_adults_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2020_2021_sensitive_*.csv - analyse_dataset_adults_flu_s5_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date @@ -7748,16 +5348,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2020_2021_sensitive_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_adults_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2020_2021_sensitive_*.csv - analyse_dataset_adults_covid_s5_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season5_start_date season5_end_date sensitive primary adults s5 2020_2021 sensitive primary season5_start_date @@ -7817,16 +5407,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2021_2022_sensitive_*.csv - analyse_dataset_adults_rsv_further_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season6_start_date - season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_adults_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2021_2022_sensitive_*.csv - analyse_dataset_adults_flu_s6_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date @@ -7857,16 +5437,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2021_2022_sensitive_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_adults_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2021_2022_sensitive_*.csv - analyse_dataset_adults_covid_s6_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season6_start_date season6_end_date sensitive primary adults s6 2021_2022 sensitive primary season6_start_date @@ -7926,16 +5496,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_adults_2022_2023_sensitive_*.csv - analyse_dataset_adults_rsv_further_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R adults season7_start_date - season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_adults_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_adults_2022_2023_sensitive_*.csv - analyse_dataset_adults_flu_s7_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date @@ -7966,16 +5526,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_adults_2022_2023_sensitive_*.csv - analyse_dataset_adults_overall_and_all_cause_further_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_adults_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_adults_2022_2023_sensitive_*.csv - analyse_dataset_adults_covid_s7_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R adults season7_start_date season7_end_date sensitive primary adults s7 2022_2023 sensitive primary season7_start_date @@ -8042,16 +5592,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2016_2017_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season1_start_date season1_end_date sensitive primary children_and_adolescents - s1 2016_2017 sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2016_2017_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s1_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season1_start_date season1_end_date sensitive primary children_and_adolescents @@ -8082,16 +5622,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2016_2017_sensitive_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season1_start_date season1_end_date sensitive primary - children_and_adolescents s1 2016_2017 sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2016_2017_sensitive_*.csv - generate_dataset_children_and_adolescents_s2_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -8133,16 +5663,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2017_2018_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season2_start_date season2_end_date sensitive primary children_and_adolescents - s2 2017_2018 sensitive primary season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2017_2018_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s2_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season2_start_date season2_end_date sensitive primary children_and_adolescents @@ -8173,16 +5693,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2017_2018_sensitive_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season2_start_date season2_end_date sensitive primary - children_and_adolescents s2 2017_2018 sensitive primary season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2017_2018_sensitive_*.csv - generate_dataset_children_and_adolescents_s3_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -8224,16 +5734,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2018_2019_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season3_start_date season3_end_date sensitive primary children_and_adolescents - s3 2018_2019 sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2018_2019_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s3_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season3_start_date season3_end_date sensitive primary children_and_adolescents @@ -8264,16 +5764,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2018_2019_sensitive_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season3_start_date season3_end_date sensitive primary - children_and_adolescents s3 2018_2019 sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2018_2019_sensitive_*.csv - generate_dataset_children_and_adolescents_s4_sensitive_primary: run: |- ehrql:v1 generate-dataset analysis/dataset_definition.py @@ -8315,16 +5805,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2019_2020_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season4_start_date season4_end_date sensitive primary children_and_adolescents - s4 2019_2020 sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_children_and_adolescents_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2019_2020_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s4_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season4_start_date season4_end_date sensitive primary children_and_adolescents @@ -8355,16 +5835,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2019_2020_sensitive_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season4_start_date season4_end_date sensitive primary - children_and_adolescents s4 2019_2020 sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_children_and_adolescents_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2019_2020_sensitive_*.csv - analyse_dataset_children_and_adolescents_covid_s4_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season4_start_date season4_end_date sensitive primary children_and_adolescents @@ -8426,16 +5896,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2020_2021_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season5_start_date season5_end_date sensitive primary children_and_adolescents - s5 2020_2021 sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_children_and_adolescents_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2020_2021_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s5_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season5_start_date season5_end_date sensitive primary children_and_adolescents @@ -8466,16 +5926,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2020_2021_sensitive_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season5_start_date season5_end_date sensitive primary - children_and_adolescents s5 2020_2021 sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_children_and_adolescents_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2020_2021_sensitive_*.csv - analyse_dataset_children_and_adolescents_covid_s5_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season5_start_date season5_end_date sensitive primary children_and_adolescents @@ -8537,16 +5987,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2021_2022_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season6_start_date season6_end_date sensitive primary children_and_adolescents - s6 2021_2022 sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_children_and_adolescents_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2021_2022_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s6_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season6_start_date season6_end_date sensitive primary children_and_adolescents @@ -8577,16 +6017,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2021_2022_sensitive_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season6_start_date season6_end_date sensitive primary - children_and_adolescents s6 2021_2022 sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_children_and_adolescents_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2021_2022_sensitive_*.csv - analyse_dataset_children_and_adolescents_covid_s6_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season6_start_date season6_end_date sensitive primary children_and_adolescents @@ -8648,16 +6078,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_primary/*_children_and_adolescents_2022_2023_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_models_master.R children_and_adolescents - season7_start_date season7_end_date sensitive primary children_and_adolescents - s7 2022_2023 sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_children_and_adolescents_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_primary/further_*_children_and_adolescents_2022_2023_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s7_sensitive_primary: run: r:latest analysis/outcome_flu/flu_models_master.R children_and_adolescents season7_start_date season7_end_date sensitive primary children_and_adolescents @@ -8688,16 +6108,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_primary/*_children_and_adolescents_2022_2023_sensitive_*.csv - analyse_dataset_children_and_adolescents_overall_and_all_cause_further_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_models_master.R - children_and_adolescents season7_start_date season7_end_date sensitive primary - children_and_adolescents s7 2022_2023 sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_children_and_adolescents_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_primary/further_*_children_and_adolescents_2022_2023_sensitive_*.csv - analyse_dataset_children_and_adolescents_covid_s7_sensitive_primary: run: r:latest analysis/outcome_covid/covid_models_master.R children_and_adolescents season7_start_date season7_end_date sensitive primary children_and_adolescents @@ -8962,222 +6372,12 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_s1_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_s1_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_flu_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s1_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date sensitive primary infants s1 2016_2017 sensitive - primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_full_s1_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_flu_full_s1_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season1_start_date - season1_end_date sensitive primary infants s1 2016_2017 sensitive primary season1_start_date - season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2016_2017_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s1_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season1_start_date season1_end_date sensitive primary infants s1 2016_2017 - sensitive primary season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_primary.csv - - generate_dataset_infants_s2_sensitive_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2017_2018_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow - -- infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date season2_end_date + generate_dataset_infants_s2_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2017_2018_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2017_2018.arrow + -- infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date season2_end_date outputs: highly_sensitive: dataset: output/data/input_infants_2017_2018_sensitive_primary.arrow @@ -9412,335 +6612,125 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary + generate_dataset_infants_s3_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2018_2019_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow + -- infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date season3_end_date outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + highly_sensitive: + dataset: output/data/input_infants_2018_2019_sensitive_primary.arrow - analyse_dataset_infants_further_flu_ethnicity_s2_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date + process_dataset_infants_s3_sensitive_primary: + run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date + sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - generate_dataset_infants_s3_sensitive_primary + - process_household_information_s3 outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + highly_sensitive: + cohort: output/data/input_processed_infants_2018_2019_sensitive_primary.arrow - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 - sensitive primary season2_start_date season2_end_date + describe_dataset_infants_s3_sensitive_primary: + run: r:latest analysis/report.R infants season3_start_date season3_end_date sensitive + primary infants s3 2018_2019 sensitive primary season3_start_date season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/rates/rates_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ses_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date + analyse_dataset_infants_rsv_ethnicity_s3_sensitive_primary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_flu_ses_s2_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date + analyse_dataset_infants_flu_ethnicity_s3_sensitive_primary: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 - sensitive primary season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_primary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date + analyse_dataset_infants_rsv_ses_s3_sensitive_primary: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date + analyse_dataset_infants_flu_ses_s3_sensitive_primary: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_sensitive_primary: - 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 sensitive primary infants s2 2017_2018 - sensitive primary season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_primary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_ses_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive - primary season2_start_date season2_end_date + analyse_dataset_infants_rsv_hh_comp_s3_sensitive_primary: + run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_flu_ethnicity_ses_s2_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive - primary season2_start_date season2_end_date + analyse_dataset_infants_flu_hh_comp_s3_sensitive_primary: + run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season3_start_date + season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date + season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv + csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_primary: - 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 sensitive primary infants s2 2017_2018 - sensitive primary season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_primary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_hh_comp_models.R + infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 + sensitive primary season3_start_date season3_end_date needs: - - process_dataset_infants_s2_sensitive_primary + - process_dataset_infants_s3_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive - primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date sensitive primary infants s2 2017_2018 sensitive - primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 - sensitive primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 - sensitive primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_full_s2_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_flu_full_s2_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season2_start_date - season2_end_date sensitive primary infants s2 2017_2018 sensitive primary season2_start_date - season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2017_2018_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s2_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season2_start_date season2_end_date sensitive primary infants s2 2017_2018 - sensitive primary season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_primary.csv - - generate_dataset_infants_s3_sensitive_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2018_2019_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2018_2019.arrow - -- infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date season3_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2018_2019_sensitive_primary.arrow - - process_dataset_infants_s3_sensitive_primary: - run: r:latest analysis/data_processing.R infants season3_start_date season3_end_date - sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - generate_dataset_infants_s3_sensitive_primary - - process_household_information_s3 - outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2018_2019_sensitive_primary.arrow - - describe_dataset_infants_s3_sensitive_primary: - run: r:latest analysis/report.R infants season3_start_date season3_end_date sensitive - primary infants s3 2018_2019 sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_rsv_ethnicity_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_flu_ethnicity_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_rsv_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_flu_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_rsv_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_flu_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_hh_comp_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv analyse_dataset_infants_rsv_ethnicity_ses_s3_sensitive_primary: run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season3_start_date @@ -9862,295 +6852,85 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date + generate_dataset_infants_s4_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2019_2020_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow + -- infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date + outputs: + highly_sensitive: + dataset: output/data/input_infants_2019_2020_sensitive_primary.arrow + + process_dataset_infants_s4_sensitive_primary: + run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date + sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_sensitive_primary + - generate_dataset_infants_s4_sensitive_primary + - process_household_information_s4 outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + highly_sensitive: + cohort: output/data/input_processed_infants_2019_2020_sensitive_primary.arrow - analyse_dataset_infants_further_flu_ethnicity_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date + describe_dataset_infants_s4_sensitive_primary: + run: r:latest analysis/report.R infants season4_start_date season4_end_date sensitive + primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date needs: - - process_dataset_infants_s3_sensitive_primary + - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + csv: output/results/rates/rates_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date + analyse_dataset_infants_rsv_ethnicity_s4_sensitive_primary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_sensitive_primary + - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_primary.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date + analyse_dataset_infants_flu_ethnicity_s4_sensitive_primary: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_sensitive_primary + - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_flu_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_sensitive_primary: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 + sensitive primary season4_start_date season4_end_date needs: - - process_dataset_infants_s3_sensitive_primary + - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date + analyse_dataset_infants_rsv_ses_s4_sensitive_primary: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_sensitive_primary + - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_primary.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date + analyse_dataset_infants_flu_ses_s4_sensitive_primary: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season4_start_date + season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date + season4_end_date needs: - - process_dataset_infants_s3_sensitive_primary + - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_flu_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive - primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive - primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive - primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date sensitive primary infants s3 2018_2019 sensitive - primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_full_s3_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_flu_full_s3_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season3_start_date - season3_end_date sensitive primary infants s3 2018_2019 sensitive primary season3_start_date - season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s3_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season3_start_date season3_end_date sensitive primary infants s3 2018_2019 - sensitive primary season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_primary.csv - - generate_dataset_infants_s4_sensitive_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2019_2020_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2019_2020.arrow - -- infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2019_2020_sensitive_primary.arrow - - process_dataset_infants_s4_sensitive_primary: - run: r:latest analysis/data_processing.R infants season4_start_date season4_end_date - sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - generate_dataset_infants_s4_sensitive_primary - - process_household_information_s4 - outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2019_2020_sensitive_primary.arrow - - describe_dataset_infants_s4_sensitive_primary: - run: r:latest analysis/report.R infants season4_start_date season4_end_date sensitive - primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_rsv_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_flu_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_rsv_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_flu_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/flu_ses_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_sensitive_primary.csv analyse_dataset_infants_overall_and_all_cause_ses_s4_sensitive_primary: run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R @@ -10312,402 +7092,122 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season4_start_date + analyse_dataset_infants_covid_ethnicity_s4_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season4_start_date + analyse_dataset_infants_covid_ses_s4_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season4_start_date + analyse_dataset_infants_covid_hh_comp_s4_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_flu_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season4_start_date + analyse_dataset_infants_covid_ethnicity_ses_s4_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s4_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive + primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_covid_ses_hh_comp_s4_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_covid_full_s4_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2019_2020_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary + generate_dataset_infants_s5_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2020_2021_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow + -- infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv + highly_sensitive: + dataset: output/data/input_infants_2020_2021_sensitive_primary.arrow - analyse_dataset_infants_further_rsv_ethnicity_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date + process_dataset_infants_s5_sensitive_primary: + run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date + sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date needs: - - process_dataset_infants_s4_sensitive_primary + - generate_dataset_infants_s5_sensitive_primary + - process_household_information_s5 outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + highly_sensitive: + cohort: output/data/input_processed_infants_2020_2021_sensitive_primary.arrow - analyse_dataset_infants_further_flu_ethnicity_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date + describe_dataset_infants_s5_sensitive_primary: + run: r:latest analysis/report.R infants season5_start_date season5_end_date sensitive + primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date needs: - - process_dataset_infants_s4_sensitive_primary + - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/rates/rates_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date + analyse_dataset_infants_rsv_ethnicity_s5_sensitive_primary: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date needs: - - process_dataset_infants_s4_sensitive_primary + - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date + analyse_dataset_infants_flu_ethnicity_s5_sensitive_primary: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season5_start_date + season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date + season5_end_date needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_full_s4_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_flu_full_s4_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s4_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_covid_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_covid_full_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date sensitive primary infants s4 2019_2020 - sensitive primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season4_start_date season4_end_date sensitive primary infants s4 2019_2020 sensitive - primary season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_primary.csv - - analyse_dataset_infants_further_covid_full_s4_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season4_start_date - season4_end_date sensitive primary infants s4 2019_2020 sensitive primary season4_start_date - season4_end_date - needs: - - process_dataset_infants_s4_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2019_2020_sensitive_primary.csv - - generate_dataset_infants_s5_sensitive_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2020_2021_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2020_2021.arrow - -- infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2020_2021_sensitive_primary.arrow - - process_dataset_infants_s5_sensitive_primary: - run: r:latest analysis/data_processing.R infants season5_start_date season5_end_date - sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - generate_dataset_infants_s5_sensitive_primary - - process_household_information_s5 - outputs: - highly_sensitive: - cohort: output/data/input_processed_infants_2020_2021_sensitive_primary.arrow - - describe_dataset_infants_s5_sensitive_primary: - run: r:latest analysis/report.R infants season5_start_date season5_end_date sensitive - primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_rsv_ethnicity_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_flu_ethnicity_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary + - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv @@ -10902,355 +7402,75 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season5_start_date + analyse_dataset_infants_covid_ethnicity_s5_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season5_start_date + analyse_dataset_infants_covid_ses_s5_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season5_start_date + analyse_dataset_infants_covid_hh_comp_s5_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_flu_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season5_start_date + analyse_dataset_infants_covid_ethnicity_ses_s5_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s5_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive + primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season5_start_date + analyse_dataset_infants_covid_ses_hh_comp_s5_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season5_start_date + analyse_dataset_infants_covid_full_s5_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_full_s5_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_flu_full_s5_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s5_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_covid_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_covid_full_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season5_start_date season5_end_date sensitive primary infants s5 2020_2021 - sensitive primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season5_start_date season5_end_date sensitive primary infants s5 2020_2021 sensitive - primary season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_primary.csv - - analyse_dataset_infants_further_covid_full_s5_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season5_start_date - season5_end_date sensitive primary infants s5 2020_2021 sensitive primary season5_start_date - season5_end_date - needs: - - process_dataset_infants_s5_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_sensitive_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2020_2021_sensitive_primary.csv generate_dataset_infants_s6_sensitive_primary: run: |- @@ -11492,365 +7712,85 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season6_start_date + analyse_dataset_infants_covid_ethnicity_s6_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s6_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season6_start_date + analyse_dataset_infants_covid_ses_s6_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season6_start_date + analyse_dataset_infants_covid_hh_comp_s6_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_flu_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season6_start_date + analyse_dataset_infants_covid_ethnicity_ses_s6_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s6_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive + primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2021_2022_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season6_start_date + analyse_dataset_infants_covid_ses_hh_comp_s6_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season6_start_date + analyse_dataset_infants_covid_full_s6_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2021_2022_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary + generate_dataset_infants_s7_sensitive_primary: + run: |- + ehrql:v1 generate-dataset analysis/dataset_definition.py + --output output/data/input_infants_2022_2023_sensitive_primary.arrow + --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow + -- infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_full_s6_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_flu_full_s6_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s6_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_covid_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_covid_full_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date sensitive primary infants s6 2021_2022 - sensitive primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season6_start_date season6_end_date sensitive primary infants s6 2021_2022 sensitive - primary season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_primary.csv - - analyse_dataset_infants_further_covid_full_s6_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season6_start_date - season6_end_date sensitive primary infants s6 2021_2022 sensitive primary season6_start_date - season6_end_date - needs: - - process_dataset_infants_s6_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2021_2022_sensitive_primary.csv - - generate_dataset_infants_s7_sensitive_primary: - run: |- - ehrql:v1 generate-dataset analysis/dataset_definition.py - --output output/data/input_infants_2022_2023_sensitive_primary.arrow - --dummy-data-file analysis/dummydata/dummyextract_infants_2022_2023.arrow - -- infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date - outputs: - highly_sensitive: - dataset: output/data/input_infants_2022_2023_sensitive_primary.arrow + highly_sensitive: + dataset: output/data/input_infants_2022_2023_sensitive_primary.arrow process_dataset_infants_s7_sensitive_primary: run: r:latest analysis/data_processing.R infants season7_start_date season7_end_date @@ -12082,362 +8022,82 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ethnicity_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season7_start_date + analyse_dataset_infants_covid_ethnicity_s7_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_flu_ethnicity_s7_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season7_start_date + analyse_dataset_infants_covid_ses_s7_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv + csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_rsv_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season7_start_date + analyse_dataset_infants_covid_hh_comp_s7_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_flu_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season7_start_date + analyse_dataset_infants_covid_ethnicity_ses_s7_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s7_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive + primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2022_2023_sensitive_primary.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_rsv_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season7_start_date + analyse_dataset_infants_covid_ses_hh_comp_s7_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_flu_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season7_start_date + analyse_dataset_infants_covid_full_s7_sensitive_primary: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date season7_end_date needs: - process_dataset_infants_s7_sensitive_primary outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv + csv: output/results/models/covid_full_model_outputs_infants_2022_2023_sensitive_primary.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_rsv_full_s7_sensitive_primary: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_flu_full_s7_sensitive_primary: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s7_sensitive_primary: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_covid_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_covid_ses_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_covid_full_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infantsfurther__covid_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_covid_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date sensitive primary infants s7 2022_2023 - sensitive primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season7_start_date season7_end_date sensitive primary infants s7 2022_2023 sensitive - primary season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_primary.csv - - analyse_dataset_infants_further_covid_full_s7_sensitive_primary: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season7_start_date - season7_end_date sensitive primary infants s7 2022_2023 sensitive primary season7_start_date - season7_end_date - needs: - - process_dataset_infants_s7_sensitive_primary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2022_2023_sensitive_primary.csv - - ## # # # # # # # # # # # # # # # # # # # - ## DESCRIPTIVE ANALYSES - ## # # # # # # # # # # # # # # # # # # # - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Older Adults - ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## DESCRIPTIVE ANALYSES + ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults + ## # # # # # # # # # # # # # # # # # # # generate_dataset_older_adults_s1_specific_secondary: run: |- @@ -13359,16 +9019,6 @@ actions: 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 @@ -13379,16 +9029,6 @@ actions: 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 - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2017_2018_specific_*.csv - 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 @@ -13440,16 +9080,6 @@ actions: 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 - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_older_adults_2018_2019_specific_*.csv - 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 @@ -13501,16 +9131,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_model_outputs_older_adults_2020_2021_specific_secondary.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/further_overall_and_all_cause_model_outputs_older_adults_2020_2021_specific_secondary.csv - ## # # # # # # # # # # # # # # # # # # # ## Cohort: Adults, Codelist Type: Specific, Investigation Type: Secondary ## # # # # # # # # # # # # # # # # # # # @@ -13545,16 +9165,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_secondary/*_adults_2017_2018_specific_*.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 - outputs: - moderately_sensitive: - csv: output/results/models/rsv_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 @@ -13565,16 +9175,6 @@ actions: 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 - 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 @@ -13625,16 +9225,6 @@ actions: 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 - 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 @@ -13685,16 +9275,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_model_outputs_adults_2020_2021_specific_secondary.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/further_overall_and_all_cause_model_outputs_adults_2020_2021_specific_secondary.csv - ## # # # # # # # # # # # # # # # # # # # ## Cohort: Children and Adolescents, Codelist Type: Specific, Investigation Type: Secondary @@ -13731,16 +9311,6 @@ actions: 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_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 @@ -13752,17 +9322,6 @@ actions: 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 - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2017_2018_specific_*.csv - 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 @@ -13815,17 +9374,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_secondary/*_children_and_adolescents_2018_2019_specific_*.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 - season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_secondary/further_*_children_and_adolescents_2018_2019_specific_*.csv - 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 @@ -13878,17 +9426,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_model_outputs_children_and_adolescents_2020_2021_specific_secondary.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 - needs: - - process_dataset_children_and_adolescents_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_model_outputs_children_and_adolescents_2020_2021_specific_secondary.csv - ## # # # # # # # # # # # # # # # # # # # ## Cohort: Infants, Codelist Type: Specific, Investigation Type: Secondary @@ -14055,146 +9592,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_secondary.csv - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_specific_secondary.csv - - 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: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_specific_secondary.csv - - 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: - - process_dataset_infants_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_specific_secondary.csv - - 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_s2_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_secondary.csv - 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 @@ -14355,146 +9752,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_secondary.csv - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - - 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: - - process_dataset_infants_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_specific_secondary.csv - - 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_s3_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_secondary.csv - 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 @@ -14585,95 +9842,25 @@ actions: moderately_sensitive: csv: output/results/models/covid_full_model_outputs_infants_2020_2021_specific_secondary.csv - 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 + 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_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv - 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 + 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_infants_s5_specific_secondary outputs: moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_infants_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_infants_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_infants_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_infants_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_infants_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_infants_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_infants_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_secondary.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_secondary.csv 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 @@ -14725,76 +9912,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_secondary.csv - 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_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_specific_secondary.csv - - 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/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_specific_secondary.csv - - 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_s5_specific_secondary - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_secondary.csv - ## # # # # # # # # # # # # # # # # # # # ## EXPLORATORY ANALYSES ## # # # # # # # # # # # # # # # # # # # @@ -15124,7 +10241,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2016_2017_specific_sensitivity.csv + csv: output/input_processed_older_adults_2016_2017_specific_sensitivity.csv describe_dataset_older_adults_s1_specific_sensitivity: run: r:latest analysis/report.R older_adults season1_start_date season1_end_date @@ -15146,16 +10263,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2016_2017_specific_*.csv - analyse_dataset_older_adults_rsv_further_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season1_start_date - season1_end_date specific sensitivity older_adults s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2016_2017_specific_*.csv - analyse_dataset_older_adults_flu_s1_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season1_start_date season1_end_date specific sensitivity older_adults s1 2016_2017 specific sensitivity @@ -15205,7 +10312,7 @@ actions: - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2017_2018_specific_sensitivity.csv + csv: output/input_processed_older_adults_2017_2018_specific_sensitivity.csv describe_dataset_older_adults_s2_specific_sensitivity: run: r:latest analysis/report.R older_adults season2_start_date season2_end_date @@ -15227,16 +10334,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2017_2018_specific_*.csv - analyse_dataset_older_adults_rsv_further_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season2_start_date - season2_end_date specific sensitivity older_adults s2 2017_2018 specific sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2017_2018_specific_*.csv - analyse_dataset_older_adults_flu_s2_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season2_start_date season2_end_date specific sensitivity older_adults s2 2017_2018 specific sensitivity @@ -15286,7 +10383,7 @@ actions: - process_household_information_s3 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2018_2019_specific_sensitivity.csv + csv: output/input_processed_older_adults_2018_2019_specific_sensitivity.csv describe_dataset_older_adults_s3_specific_sensitivity: run: r:latest analysis/report.R older_adults season3_start_date season3_end_date @@ -15308,16 +10405,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2018_2019_specific_*.csv - analyse_dataset_older_adults_rsv_further_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season3_start_date - season3_end_date specific sensitivity older_adults s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2018_2019_specific_*.csv - analyse_dataset_older_adults_flu_s3_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season3_start_date season3_end_date specific sensitivity older_adults s3 2018_2019 specific sensitivity @@ -15367,7 +10454,7 @@ actions: - process_household_information_s4 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2019_2020_specific_sensitivity.csv + csv: output/input_processed_older_adults_2019_2020_specific_sensitivity.csv describe_dataset_older_adults_s4_specific_sensitivity: run: r:latest analysis/report.R older_adults season4_start_date season4_end_date @@ -15389,16 +10476,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2019_2020_specific_*.csv - analyse_dataset_older_adults_rsv_further_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season4_start_date - season4_end_date specific sensitivity older_adults s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2019_2020_specific_*.csv - analyse_dataset_older_adults_flu_s4_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season4_start_date season4_end_date specific sensitivity older_adults s4 2019_2020 specific sensitivity @@ -15468,7 +10545,7 @@ actions: - process_household_information_s5 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2020_2021_specific_sensitivity.csv + csv: output/input_processed_older_adults_2020_2021_specific_sensitivity.csv describe_dataset_older_adults_s5_specific_sensitivity: run: r:latest analysis/report.R older_adults season5_start_date season5_end_date @@ -15490,16 +10567,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2020_2021_specific_*.csv - analyse_dataset_older_adults_rsv_further_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season5_start_date - season5_end_date specific sensitivity older_adults s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2020_2021_specific_*.csv - analyse_dataset_older_adults_flu_s5_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season5_start_date season5_end_date specific sensitivity older_adults s5 2020_2021 specific sensitivity @@ -15569,7 +10636,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2021_2022_specific_sensitivity.csv + csv: output/input_processed_older_adults_2021_2022_specific_sensitivity.csv describe_dataset_older_adults_s6_specific_sensitivity: run: r:latest analysis/report.R older_adults season6_start_date season6_end_date @@ -15591,16 +10658,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2021_2022_specific_*.csv - analyse_dataset_older_adults_rsv_further_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season6_start_date - season6_end_date specific sensitivity older_adults s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2021_2022_specific_*.csv - analyse_dataset_older_adults_flu_s6_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season6_start_date season6_end_date specific sensitivity older_adults s6 2021_2022 specific sensitivity @@ -15670,7 +10727,7 @@ actions: - process_household_information_s7 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2022_2023_specific_sensitivity.csv + csv: output/input_processed_older_adults_2022_2023_specific_sensitivity.csv describe_dataset_older_adults_s7_specific_sensitivity: run: r:latest analysis/report.R older_adults season7_start_date season7_end_date @@ -15692,16 +10749,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2022_2023_specific_*.csv - analyse_dataset_older_adults_rsv_further_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season7_start_date - season7_end_date specific sensitivity older_adults s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2022_2023_specific_*.csv - analyse_dataset_older_adults_flu_s7_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season7_start_date season7_end_date specific sensitivity older_adults s7 2022_2023 specific sensitivity @@ -15775,7 +10822,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2016_2017_specific_sensitivity.csv + csv: output/input_processed_adults_2016_2017_specific_sensitivity.csv describe_dataset_adults_s1_specific_sensitivity: run: r:latest analysis/report.R adults season1_start_date season1_end_date specific @@ -15796,16 +10843,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2016_2017_specific_*.csv - analyse_dataset_adults_rsv_further_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season1_start_date - season1_end_date specific sensitivity adults s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_adults_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2016_2017_specific_*.csv - analyse_dataset_adults_flu_s1_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season1_start_date season1_end_date specific sensitivity adults s1 2016_2017 specific sensitivity season1_start_date @@ -15855,7 +10892,7 @@ actions: - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2017_2018_specific_sensitivity.csv + csv: output/input_processed_adults_2017_2018_specific_sensitivity.csv describe_dataset_adults_s2_specific_sensitivity: run: r:latest analysis/report.R adults season2_start_date season2_end_date specific @@ -15876,16 +10913,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2017_2018_specific_*.csv - analyse_dataset_adults_rsv_further_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season2_start_date - season2_end_date specific sensitivity adults s2 2017_2018 specific sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_adults_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2017_2018_specific_*.csv - analyse_dataset_adults_flu_s2_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season2_start_date season2_end_date specific sensitivity adults s2 2017_2018 specific sensitivity season2_start_date @@ -15935,7 +10962,7 @@ actions: - process_household_information_s3 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2018_2019_specific_sensitivity.csv + csv: output/input_processed_adults_2018_2019_specific_sensitivity.csv describe_dataset_adults_s3_specific_sensitivity: run: r:latest analysis/report.R adults season3_start_date season3_end_date specific @@ -15956,16 +10983,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2018_2019_specific_*.csv - analyse_dataset_adults_rsv_further_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season3_start_date - season3_end_date specific sensitivity adults s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_adults_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2018_2019_specific_*.csv - analyse_dataset_adults_flu_s3_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season3_start_date season3_end_date specific sensitivity adults s3 2018_2019 specific sensitivity season3_start_date @@ -16015,7 +11032,7 @@ actions: - process_household_information_s4 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2019_2020_specific_sensitivity.csv + csv: output/input_processed_adults_2019_2020_specific_sensitivity.csv describe_dataset_adults_s4_specific_sensitivity: run: r:latest analysis/report.R adults season4_start_date season4_end_date specific @@ -16036,16 +11053,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2019_2020_specific_*.csv - analyse_dataset_adults_rsv_further_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season4_start_date - season4_end_date specific sensitivity adults s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_adults_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2019_2020_specific_*.csv - analyse_dataset_adults_flu_s4_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season4_start_date season4_end_date specific sensitivity adults s4 2019_2020 specific sensitivity season4_start_date @@ -16115,7 +11122,7 @@ actions: - process_household_information_s5 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2020_2021_specific_sensitivity.csv + csv: output/input_processed_adults_2020_2021_specific_sensitivity.csv describe_dataset_adults_s5_specific_sensitivity: run: r:latest analysis/report.R adults season5_start_date season5_end_date specific @@ -16136,16 +11143,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2020_2021_specific_*.csv - analyse_dataset_adults_rsv_further_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season5_start_date - season5_end_date specific sensitivity adults s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_adults_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2020_2021_specific_*.csv - analyse_dataset_adults_flu_s5_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season5_start_date season5_end_date specific sensitivity adults s5 2020_2021 specific sensitivity season5_start_date @@ -16215,7 +11212,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2021_2022_specific_sensitivity.csv + csv: output/input_processed_adults_2021_2022_specific_sensitivity.csv describe_dataset_adults_s6_specific_sensitivity: run: r:latest analysis/report.R adults season6_start_date season6_end_date specific @@ -16236,16 +11233,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2021_2022_specific_*.csv - analyse_dataset_adults_rsv_further_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season6_start_date - season6_end_date specific sensitivity adults s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_adults_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2021_2022_specific_*.csv - analyse_dataset_adults_flu_s6_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season6_start_date season6_end_date specific sensitivity adults s6 2021_2022 specific sensitivity season6_start_date @@ -16315,7 +11302,7 @@ actions: - process_household_information_s7 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2022_2023_specific_sensitivity.csv + csv: output/input_processed_adults_2022_2023_specific_sensitivity.csv describe_dataset_adults_s7_specific_sensitivity: run: r:latest analysis/report.R adults season7_start_date season7_end_date specific @@ -16336,16 +11323,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2022_2023_specific_*.csv - analyse_dataset_adults_rsv_further_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season7_start_date - season7_end_date specific sensitivity adults s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_adults_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2022_2023_specific_*.csv - analyse_dataset_adults_flu_s7_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season7_start_date season7_end_date specific sensitivity adults s7 2022_2023 specific sensitivity season7_start_date @@ -16419,7 +11396,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2016_2017_specific_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2016_2017_specific_sensitivity.csv describe_dataset_children_and_adolescents_s1_specific_sensitivity: run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date @@ -16441,16 +11418,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2016_2017_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season1_start_date season1_end_date specific sensitivity children_and_adolescents - s1 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2016_2017_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s1_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season1_start_date season1_end_date specific sensitivity children_and_adolescents s1 2016_2017 @@ -16502,7 +11469,7 @@ actions: - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2017_2018_specific_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2017_2018_specific_sensitivity.csv describe_dataset_children_and_adolescents_s2_specific_sensitivity: run: r:latest analysis/report.R children_and_adolescents season2_start_date season2_end_date @@ -16524,16 +11491,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season2_start_date season2_end_date specific sensitivity children_and_adolescents - s2 2017_2018 specific sensitivity season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2017_2018_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s2_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season2_start_date season2_end_date specific sensitivity children_and_adolescents s2 2017_2018 @@ -16585,7 +11542,7 @@ actions: - process_household_information_s3 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2018_2019_specific_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2018_2019_specific_sensitivity.csv describe_dataset_children_and_adolescents_s3_specific_sensitivity: run: r:latest analysis/report.R children_and_adolescents season3_start_date season3_end_date @@ -16607,16 +11564,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season3_start_date season3_end_date specific sensitivity children_and_adolescents - s3 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2018_2019_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s3_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season3_start_date season3_end_date specific sensitivity children_and_adolescents s3 2018_2019 @@ -16668,7 +11615,7 @@ actions: - process_household_information_s4 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2019_2020_specific_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2019_2020_specific_sensitivity.csv describe_dataset_children_and_adolescents_s4_specific_sensitivity: run: r:latest analysis/report.R children_and_adolescents season4_start_date season4_end_date @@ -16690,16 +11637,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2019_2020_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season4_start_date season4_end_date specific sensitivity children_and_adolescents - s4 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_children_and_adolescents_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2019_2020_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s4_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season4_start_date season4_end_date specific sensitivity children_and_adolescents s4 2019_2020 @@ -16771,7 +11708,7 @@ actions: - process_household_information_s5 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2020_2021_specific_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2020_2021_specific_sensitivity.csv describe_dataset_children_and_adolescents_s5_specific_sensitivity: run: r:latest analysis/report.R children_and_adolescents season5_start_date season5_end_date @@ -16793,16 +11730,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2020_2021_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season5_start_date season5_end_date specific sensitivity children_and_adolescents - s5 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_children_and_adolescents_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2020_2021_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s5_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season5_start_date season5_end_date specific sensitivity children_and_adolescents s5 2020_2021 @@ -16874,7 +11801,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2021_2022_specific_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2021_2022_specific_sensitivity.csv describe_dataset_children_and_adolescents_s6_specific_sensitivity: run: r:latest analysis/report.R children_and_adolescents season6_start_date season6_end_date @@ -16896,16 +11823,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2021_2022_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season6_start_date season6_end_date specific sensitivity children_and_adolescents - s6 2021_2022 specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_children_and_adolescents_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2021_2022_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s6_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season6_start_date season6_end_date specific sensitivity children_and_adolescents s6 2021_2022 @@ -16977,7 +11894,7 @@ actions: - process_household_information_s7 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2022_2023_specific_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2022_2023_specific_sensitivity.csv describe_dataset_children_and_adolescents_s7_specific_sensitivity: run: r:latest analysis/report.R children_and_adolescents season7_start_date season7_end_date @@ -16999,16 +11916,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2022_2023_specific_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season7_start_date season7_end_date specific sensitivity children_and_adolescents - s7 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_children_and_adolescents_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2022_2023_specific_*.csv - analyse_dataset_children_and_adolescents_flu_s7_specific_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season7_start_date season7_end_date specific sensitivity children_and_adolescents s7 2022_2023 @@ -17084,7 +11991,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2016_2017_specific_sensitivity.csv + csv: output/input_processed_infants_2016_2017_specific_sensitivity.csv describe_dataset_infants_s1_specific_sensitivity: run: r:latest analysis/report.R infants season1_start_date season1_end_date specific @@ -17305,226 +12212,16 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2016_2017_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_s1_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s1_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season1_start_date season1_end_date specific sensitivity infants s1 - 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_s1_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s1_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season1_start_date season1_end_date specific sensitivity infants s1 - 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season1_start_date season1_end_date specific sensitivity infants s1 - 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season1_start_date season1_end_date specific sensitivity infants s1 2016_2017 - specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s1_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season1_start_date season1_end_date specific sensitivity infants s1 2016_2017 - specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s1_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season1_start_date season1_end_date specific sensitivity infants s1 - 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date specific sensitivity infants s1 2016_2017 - specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date specific sensitivity infants s1 2016_2017 - specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season1_start_date season1_end_date specific sensitivity infants s1 - 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s1_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season1_start_date season1_end_date specific sensitivity infants s1 - 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s1_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s1_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season1_start_date - season1_end_date specific sensitivity infants s1 2016_2017 specific sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2016_2017_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s1_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season1_start_date season1_end_date specific sensitivity infants s1 - 2016_2017 specific sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2016_2017_specific_sensitivity.csv - - process_dataset_infants_s2_specific_sensitivity: - run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season2_start_date - season2_end_date specific primary sensitivity infants s2 2017_2018 season2_start_date - season2_end_date specific primary sensitivity + process_dataset_infants_s2_specific_sensitivity: + run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season2_start_date + season2_end_date specific primary sensitivity infants s2 2017_2018 season2_start_date + season2_end_date specific primary sensitivity needs: - generate_dataset_infants_s2_specific_primary - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2017_2018_specific_sensitivity.csv + csv: output/input_processed_infants_2017_2018_specific_sensitivity.csv describe_dataset_infants_s2_specific_sensitivity: run: r:latest analysis/report.R infants season2_start_date season2_end_date specific @@ -17745,342 +12442,132 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date + process_dataset_infants_s3_specific_sensitivity: + run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season3_start_date + season3_end_date specific primary sensitivity infants s3 2018_2019 season3_start_date + season3_end_date specific primary sensitivity needs: - - process_dataset_infants_s2_specific_sensitivity + - generate_dataset_infants_s3_specific_primary + - process_household_information_s3 outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/input_processed_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_s2_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date + describe_dataset_infants_s3_specific_sensitivity: + run: r:latest analysis/report.R infants season3_start_date season3_end_date specific + sensitivity infants s3 2018_2019 specific sensitivity season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/rates/rates_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_specific_sensitivity: - 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 sensitivity infants s2 - 2017_2018 specific sensitivity season2_start_date season2_end_date + analyse_dataset_infants_rsv_ethnicity_s3_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date + analyse_dataset_infants_flu_ethnicity_s3_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ses_s2_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_specific_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season3_start_date season3_end_date specific sensitivity infants s3 + 2018_2019 specific sensitivity season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s2_specific_sensitivity: - 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 sensitivity infants s2 - 2017_2018 specific sensitivity season2_start_date season2_end_date + analyse_dataset_infants_rsv_ses_s3_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_hh_comp_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date + analyse_dataset_infants_flu_ses_s3_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_flu_hh_comp_s2_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_ses_s3_specific_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R + infants season3_start_date season3_end_date specific sensitivity infants s3 + 2018_2019 specific sensitivity season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_specific_sensitivity: - 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 sensitivity infants s2 - 2017_2018 specific sensitivity season2_start_date season2_end_date + analyse_dataset_infants_rsv_hh_comp_s3_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_ses_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season2_start_date season2_end_date specific sensitivity infants s2 2017_2018 - specific sensitivity season2_start_date season2_end_date + analyse_dataset_infants_flu_hh_comp_s3_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_ses_s2_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season2_start_date season2_end_date specific sensitivity infants s2 2017_2018 - specific sensitivity season2_start_date season2_end_date + analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_specific_sensitivity: + 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 sensitivity infants s3 + 2018_2019 specific sensitivity season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_specific_sensitivity: - 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 sensitivity infants s2 - 2017_2018 specific sensitivity season2_start_date season2_end_date + analyse_dataset_infants_rsv_ethnicity_ses_s3_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_specific_sensitivity.csv + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date specific sensitivity infants s2 2017_2018 - specific sensitivity season2_start_date season2_end_date + analyse_dataset_infants_flu_ethnicity_ses_s3_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants season3_start_date + season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity + season3_start_date season3_end_date needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s2_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date specific sensitivity infants s2 2017_2018 - specific sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_specific_sensitivity: - 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 sensitivity infants s2 - 2017_2018 specific sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s2_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_specific_sensitivity: - 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 sensitivity infants s2 - 2017_2018 specific sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s2_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s2_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season2_start_date - season2_end_date specific sensitivity infants s2 2017_2018 specific sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2017_2018_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s2_specific_sensitivity: - 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 sensitivity infants s2 - 2017_2018 specific sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_specific_sensitivity.csv - - process_dataset_infants_s3_specific_sensitivity: - run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season3_start_date - season3_end_date specific primary sensitivity infants s3 2018_2019 season3_start_date - season3_end_date specific primary sensitivity - needs: - - generate_dataset_infants_s3_specific_primary - - process_household_information_s3 - outputs: - moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2018_2019_specific_sensitivity.csv - - describe_dataset_infants_s3_specific_sensitivity: - run: r:latest analysis/report.R infants season3_start_date season3_end_date specific - sensitivity infants s3 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season3_start_date season3_end_date specific sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_rsv_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_flu_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R - infants season3_start_date season3_end_date specific sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_rsv_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_flu_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s3_specific_sensitivity outputs: moderately_sensitive: csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv @@ -18185,295 +12672,85 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date + process_dataset_infants_s4_specific_sensitivity: + run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season4_start_date + season4_end_date specific primary sensitivity infants s4 2019_2020 season4_start_date + season4_end_date specific primary sensitivity needs: - - process_dataset_infants_s3_specific_sensitivity + - generate_dataset_infants_s4_specific_primary + - process_household_information_s4 outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv + csv: output/input_processed_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date + describe_dataset_infants_s4_specific_sensitivity: + run: r:latest analysis/report.R infants season4_start_date season4_end_date specific + sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv + csv: output/results/rates/rates_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date + analyse_dataset_infants_rsv_ethnicity_s4_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season4_start_date + season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity + season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_specific_sensitivity.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date + analyse_dataset_infants_flu_ethnicity_s4_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season4_start_date + season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity + season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_specific_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season4_start_date season4_end_date specific sensitivity infants s4 + 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date + analyse_dataset_infants_rsv_ses_s4_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season4_start_date + season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity + season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date + analyse_dataset_infants_flu_ses_s4_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season4_start_date + season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity + season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv + csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_flu_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date + analyse_dataset_infants_overall_and_all_cause_ses_s4_specific_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R + infants season4_start_date season4_end_date specific sensitivity infants s4 + 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - - process_dataset_infants_s3_specific_sensitivity + - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season3_start_date season3_end_date specific sensitivity infants s3 2018_2019 - specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season3_start_date season3_end_date specific sensitivity infants s3 2018_2019 - specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date specific sensitivity infants s3 2018_2019 - specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date specific sensitivity infants s3 2018_2019 - specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s3_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s3_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season3_start_date - season3_end_date specific sensitivity infants s3 2018_2019 specific sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s3_specific_sensitivity: - 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 sensitivity infants s3 - 2018_2019 specific sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_specific_sensitivity.csv - - process_dataset_infants_s4_specific_sensitivity: - run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season4_start_date - season4_end_date specific primary sensitivity infants s4 2019_2020 season4_start_date - season4_end_date specific primary sensitivity - needs: - - generate_dataset_infants_s4_specific_primary - - process_household_information_s4 - outputs: - moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2019_2020_specific_sensitivity.csv - - describe_dataset_infants_s4_specific_sensitivity: - run: r:latest analysis/report.R infants season4_start_date season4_end_date specific - sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_rsv_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_flu_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_ses_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv analyse_dataset_infants_rsv_hh_comp_s4_specific_sensitivity: run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season4_start_date @@ -18625,420 +12902,140 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season4_start_date + analyse_dataset_infants_covid_ethnicity_s4_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season4_start_date + analyse_dataset_infants_covid_ses_s4_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season4_start_date + analyse_dataset_infants_covid_hh_comp_s4_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season4_start_date + analyse_dataset_infants_covid_ethnicity_ses_s4_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s4_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 + specific sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_covid_ses_hh_comp_s4_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_flu_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_covid_full_s4_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/covid_full_model_outputs_infants_2019_2020_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date + process_dataset_infants_s5_specific_sensitivity: + run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season5_start_date + season5_end_date specific primary sensitivity infants s5 2020_2021 season5_start_date + season5_end_date specific primary sensitivity needs: - - process_dataset_infants_s4_specific_sensitivity + - generate_dataset_infants_s5_specific_primary + - process_household_information_s5 outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/input_processed_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date + describe_dataset_infants_s5_specific_sensitivity: + run: r:latest analysis/report.R infants season5_start_date season5_end_date specific + sensitivity infants s5 2020_2021 specific sensitivity season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_sensitivity + - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/rates/rates_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date + analyse_dataset_infants_rsv_ethnicity_s5_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season5_start_date + season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity + season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_sensitivity + - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date + analyse_dataset_infants_flu_ethnicity_s5_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season5_start_date + season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity + season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_sensitivity + - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date + analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R + infants season5_start_date season5_end_date specific sensitivity infants s5 + 2020_2021 specific sensitivity season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_sensitivity + - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date + analyse_dataset_infants_rsv_ses_s5_specific_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season5_start_date + season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity + season5_start_date season5_end_date needs: - - process_dataset_infants_s4_specific_sensitivity + - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s4_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s4_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s4_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_covid_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_covid_full_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date specific sensitivity infants s4 - 2019_2020 specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season4_start_date season4_end_date specific sensitivity infants s4 2019_2020 - specific sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2019_2020_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s4_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season4_start_date - season4_end_date specific sensitivity infants s4 2019_2020 specific sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2019_2020_specific_sensitivity.csv - - process_dataset_infants_s5_specific_sensitivity: - run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season5_start_date - season5_end_date specific primary sensitivity infants s5 2020_2021 season5_start_date - season5_end_date specific primary sensitivity - needs: - - generate_dataset_infants_s5_specific_primary - - process_household_information_s5 - outputs: - moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2020_2021_specific_sensitivity.csv - - describe_dataset_infants_s5_specific_sensitivity: - run: r:latest analysis/report.R infants season5_start_date season5_end_date specific - sensitivity infants s5 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s5_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season5_start_date season5_end_date specific sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_rsv_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_flu_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/flu_ses_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date + analyse_dataset_infants_flu_ses_s5_specific_sensitivity: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season5_start_date + season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity + season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_sensitivity outputs: @@ -19205,268 +13202,58 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season5_start_date + analyse_dataset_infants_covid_ethnicity_s5_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season5_start_date + analyse_dataset_infants_covid_ses_s5_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_specific_sensitivity: - 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 sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv + csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season5_start_date + analyse_dataset_infants_covid_hh_comp_s5_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season5_start_date + analyse_dataset_infants_covid_ethnicity_ses_s5_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s5_specific_sensitivity: - 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 sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 + specific sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_specific_sensitivity: - 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 sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_specific_sensitivity: - 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 sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_specific_sensitivity: - 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 sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_specific_sensitivity: - 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 sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s5_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s5_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s5_specific_sensitivity: - 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 sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_covid_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season5_start_date + analyse_dataset_infants_covid_ses_hh_comp_s5_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity season5_start_date season5_end_date needs: @@ -19485,76 +13272,6 @@ actions: moderately_sensitive: csv: output/results/models/covid_full_model_outputs_infants_2020_2021_specific_sensitivity.csv - analyse_dataset_infants_further_covid_ethnicity_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season5_start_date season5_end_date specific sensitivity infants s5 - 2020_2021 specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season5_start_date season5_end_date specific sensitivity infants s5 2020_2021 - specific sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s5_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season5_start_date - season5_end_date specific sensitivity infants s5 2020_2021 specific sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_specific_sensitivity.csv - process_dataset_infants_s6_specific_sensitivity: run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season6_start_date season6_end_date specific primary sensitivity infants s6 2021_2022 season6_start_date @@ -19564,7 +13281,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2021_2022_specific_sensitivity.csv + csv: output/input_processed_infants_2021_2022_specific_sensitivity.csv describe_dataset_infants_s6_specific_sensitivity: run: r:latest analysis/report.R infants season6_start_date season6_end_date specific @@ -19785,375 +13502,95 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season6_start_date + analyse_dataset_infants_covid_ethnicity_s6_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_s6_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season6_start_date + analyse_dataset_infants_covid_ses_s6_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season6_start_date + analyse_dataset_infants_covid_hh_comp_s6_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season6_start_date + analyse_dataset_infants_covid_ethnicity_ses_s6_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s6_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 + specific sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season6_start_date + analyse_dataset_infants_covid_ses_hh_comp_s6_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_flu_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season6_start_date + analyse_dataset_infants_covid_full_s6_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/results/models/covid_full_model_outputs_infants_2021_2022_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date + process_dataset_infants_s7_specific_sensitivity: + run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season7_start_date + season7_end_date specific primary sensitivity infants s7 2022_2023 season7_start_date + season7_end_date specific primary sensitivity needs: - - process_dataset_infants_s6_specific_sensitivity + - generate_dataset_infants_s7_specific_primary + - process_household_information_s7 outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv + csv: output/input_processed_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date + describe_dataset_infants_s7_specific_sensitivity: + run: r:latest analysis/report.R infants season7_start_date season7_end_date specific + sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date needs: - - process_dataset_infants_s6_specific_sensitivity + - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s6_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s6_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s6_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_covid_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_covid_full_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date specific sensitivity infants s6 - 2021_2022 specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season6_start_date season6_end_date specific sensitivity infants s6 2021_2022 - specific sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2021_2022_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s6_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season6_start_date - season6_end_date specific sensitivity infants s6 2021_2022 specific sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2021_2022_specific_sensitivity.csv - - process_dataset_infants_s7_specific_sensitivity: - run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season7_start_date - season7_end_date specific primary sensitivity infants s7 2022_2023 season7_start_date - season7_end_date specific primary sensitivity - needs: - - generate_dataset_infants_s7_specific_primary - - process_household_information_s7 - outputs: - moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2022_2023_specific_sensitivity.csv - - describe_dataset_infants_s7_specific_sensitivity: - run: r:latest analysis/report.R infants season7_start_date season7_end_date specific - sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2022_2023_specific_sensitivity.csv + csv: output/results/rates/rates_infants_2022_2023_specific_sensitivity.csv analyse_dataset_infants_rsv_ethnicity_s7_specific_sensitivity: run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season7_start_date @@ -20365,359 +13802,79 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season7_start_date + analyse_dataset_infants_covid_ethnicity_s7_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2022_2023_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_s7_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season7_start_date + analyse_dataset_infants_covid_ses_s7_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_models.R infants season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_specific_sensitivity.csv + csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season7_start_date + analyse_dataset_infants_covid_hh_comp_s7_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv + csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_flu_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season7_start_date + analyse_dataset_infants_covid_ethnicity_ses_s7_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date + analyse_dataset_infants_covid_ethnicity_hh_comp_s7_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants + season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 + specific sensitivity season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv + csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_rsv_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season7_start_date + analyse_dataset_infants_covid_ses_hh_comp_s7_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv + csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_flu_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season7_start_date + analyse_dataset_infants_covid_full_s7_specific_sensitivity: + run: r:latest analysis/outcome_covid/covid_full_models.R infants season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity season7_start_date season7_end_date needs: - process_dataset_infants_s7_specific_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv + csv: output/results/models/covid_full_model_outputs_infants_2022_2023_specific_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s7_specific_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s7_specific_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s7_specific_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_covid_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_hh_comp_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_ses_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_covid_ethnicity_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_covid_ses_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_ses_hh_comp_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_covid_full_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/covid_full_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/covid_full_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date specific sensitivity infants s7 - 2022_2023 specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season7_start_date season7_end_date specific sensitivity infants s7 2022_2023 - specific sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2022_2023_specific_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s7_specific_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season7_start_date - season7_end_date specific sensitivity infants s7 2022_2023 specific sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_specific_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2022_2023_specific_sensitivity.csv - - ## # # # # # # # # # # # # # # # # # # # - ## Cohort: Older Adults, Codelist Type: Sensitive - ## # # # # # # # # # # # # # # # # # # # + ## # # # # # # # # # # # # # # # # # # # + ## Cohort: Older Adults, Codelist Type: Sensitive + ## # # # # # # # # # # # # # # # # # # # process_dataset_older_adults_s1_sensitive_sensitivity: run: r:latest analysis/sensitivity_analyses/data_processing_sens.R older_adults @@ -20728,7 +13885,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2016_2017_sensitive_sensitivity.csv + csv: output/input_processed_older_adults_2016_2017_sensitive_sensitivity.csv describe_dataset_older_adults_s1_sensitive_sensitivity: run: r:latest analysis/report.R older_adults season1_start_date season1_end_date @@ -20750,16 +13907,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2016_2017_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season1_start_date - season1_end_date sensitive sensitivity older_adults s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_older_adults_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2016_2017_sensitive_*.csv - analyse_dataset_older_adults_flu_s1_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season1_start_date season1_end_date sensitive sensitivity older_adults s1 2016_2017 sensitive sensitivity @@ -20809,7 +13956,7 @@ actions: - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2017_2018_sensitive_sensitivity.csv + csv: output/input_processed_older_adults_2017_2018_sensitive_sensitivity.csv describe_dataset_older_adults_s2_sensitive_sensitivity: run: r:latest analysis/report.R older_adults season2_start_date season2_end_date @@ -20831,16 +13978,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2017_2018_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season2_start_date - season2_end_date sensitive sensitivity older_adults s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_older_adults_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2017_2018_sensitive_*.csv - analyse_dataset_older_adults_flu_s2_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season2_start_date season2_end_date sensitive sensitivity older_adults s2 2017_2018 sensitive sensitivity @@ -20890,7 +14027,7 @@ actions: - process_household_information_s3 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2018_2019_sensitive_sensitivity.csv + csv: output/input_processed_older_adults_2018_2019_sensitive_sensitivity.csv describe_dataset_older_adults_s3_sensitive_sensitivity: run: r:latest analysis/report.R older_adults season3_start_date season3_end_date @@ -20912,16 +14049,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2018_2019_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season3_start_date - season3_end_date sensitive sensitivity older_adults s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_older_adults_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2018_2019_sensitive_*.csv - analyse_dataset_older_adults_flu_s3_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season3_start_date season3_end_date sensitive sensitivity older_adults s3 2018_2019 sensitive sensitivity @@ -20971,7 +14098,7 @@ actions: - process_household_information_s4 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2019_2020_sensitive_sensitivity.csv + csv: output/input_processed_older_adults_2019_2020_sensitive_sensitivity.csv describe_dataset_older_adults_s4_sensitive_sensitivity: run: r:latest analysis/report.R older_adults season4_start_date season4_end_date @@ -20993,16 +14120,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2019_2020_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season4_start_date - season4_end_date sensitive sensitivity older_adults s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_older_adults_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2019_2020_sensitive_*.csv - analyse_dataset_older_adults_flu_s4_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season4_start_date season4_end_date sensitive sensitivity older_adults s4 2019_2020 sensitive sensitivity @@ -21072,7 +14189,7 @@ actions: - process_household_information_s5 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2020_2021_sensitive_sensitivity.csv + csv: output/input_processed_older_adults_2020_2021_sensitive_sensitivity.csv describe_dataset_older_adults_s5_sensitive_sensitivity: run: r:latest analysis/report.R older_adults season5_start_date season5_end_date @@ -21094,16 +14211,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2020_2021_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season5_start_date - season5_end_date sensitive sensitivity older_adults s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_older_adults_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2020_2021_sensitive_*.csv - analyse_dataset_older_adults_flu_s5_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season5_start_date season5_end_date sensitive sensitivity older_adults s5 2020_2021 sensitive sensitivity @@ -21173,7 +14280,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2021_2022_sensitive_sensitivity.csv + csv: output/input_processed_older_adults_2021_2022_sensitive_sensitivity.csv describe_dataset_older_adults_s6_sensitive_sensitivity: run: r:latest analysis/report.R older_adults season6_start_date season6_end_date @@ -21195,16 +14302,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2021_2022_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season6_start_date - season6_end_date sensitive sensitivity older_adults s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_older_adults_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2021_2022_sensitive_*.csv - analyse_dataset_older_adults_flu_s6_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season6_start_date season6_end_date sensitive sensitivity older_adults s6 2021_2022 sensitive sensitivity @@ -21274,7 +14371,7 @@ actions: - process_household_information_s7 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_older_adults_2022_2023_sensitive_sensitivity.csv + csv: output/input_processed_older_adults_2022_2023_sensitive_sensitivity.csv describe_dataset_older_adults_s7_sensitive_sensitivity: run: r:latest analysis/report.R older_adults season7_start_date season7_end_date @@ -21296,16 +14393,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_older_adults_2022_2023_sensitive_*.csv - analyse_dataset_older_adults_rsv_further_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R older_adults season7_start_date - season7_end_date sensitive sensitivity older_adults s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_older_adults_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_older_adults_2022_2023_sensitive_*.csv - analyse_dataset_older_adults_flu_s7_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R older_adults season7_start_date season7_end_date sensitive sensitivity older_adults s7 2022_2023 sensitive sensitivity @@ -21379,7 +14466,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2016_2017_sensitive_sensitivity.csv + csv: output/input_processed_adults_2016_2017_sensitive_sensitivity.csv describe_dataset_adults_s1_sensitive_sensitivity: run: r:latest analysis/report.R adults season1_start_date season1_end_date sensitive @@ -21400,16 +14487,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2016_2017_sensitive_*.csv - analyse_dataset_adults_rsv_further_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season1_start_date - season1_end_date sensitive sensitivity adults s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_adults_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2016_2017_sensitive_*.csv - analyse_dataset_adults_flu_s1_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season1_start_date season1_end_date sensitive sensitivity adults s1 2016_2017 sensitive sensitivity season1_start_date @@ -21459,7 +14536,7 @@ actions: - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2017_2018_sensitive_sensitivity.csv + csv: output/input_processed_adults_2017_2018_sensitive_sensitivity.csv describe_dataset_adults_s2_sensitive_sensitivity: run: r:latest analysis/report.R adults season2_start_date season2_end_date sensitive @@ -21480,16 +14557,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2017_2018_sensitive_*.csv - analyse_dataset_adults_rsv_further_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season2_start_date - season2_end_date sensitive sensitivity adults s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_adults_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2017_2018_sensitive_*.csv - analyse_dataset_adults_flu_s2_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season2_start_date season2_end_date sensitive sensitivity adults s2 2017_2018 sensitive sensitivity season2_start_date @@ -21539,7 +14606,7 @@ actions: - process_household_information_s3 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2018_2019_sensitive_sensitivity.csv + csv: output/input_processed_adults_2018_2019_sensitive_sensitivity.csv describe_dataset_adults_s3_sensitive_sensitivity: run: r:latest analysis/report.R adults season3_start_date season3_end_date sensitive @@ -21560,16 +14627,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2018_2019_sensitive_*.csv - analyse_dataset_adults_rsv_further_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season3_start_date - season3_end_date sensitive sensitivity adults s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_adults_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2018_2019_sensitive_*.csv - analyse_dataset_adults_flu_s3_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season3_start_date season3_end_date sensitive sensitivity adults s3 2018_2019 sensitive sensitivity season3_start_date @@ -21619,7 +14676,7 @@ actions: - process_household_information_s4 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2019_2020_sensitive_sensitivity.csv + csv: output/input_processed_adults_2019_2020_sensitive_sensitivity.csv describe_dataset_adults_s4_sensitive_sensitivity: run: r:latest analysis/report.R adults season4_start_date season4_end_date sensitive @@ -21640,16 +14697,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2019_2020_sensitive_*.csv - analyse_dataset_adults_rsv_further_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season4_start_date - season4_end_date sensitive sensitivity adults s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_adults_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2019_2020_sensitive_*.csv - analyse_dataset_adults_flu_s4_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season4_start_date season4_end_date sensitive sensitivity adults s4 2019_2020 sensitive sensitivity season4_start_date @@ -21719,7 +14766,7 @@ actions: - process_household_information_s5 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2020_2021_sensitive_sensitivity.csv + csv: output/input_processed_adults_2020_2021_sensitive_sensitivity.csv describe_dataset_adults_s5_sensitive_sensitivity: run: r:latest analysis/report.R adults season5_start_date season5_end_date sensitive @@ -21740,16 +14787,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2020_2021_sensitive_*.csv - analyse_dataset_adults_rsv_further_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season5_start_date - season5_end_date sensitive sensitivity adults s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_adults_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2020_2021_sensitive_*.csv - analyse_dataset_adults_flu_s5_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season5_start_date season5_end_date sensitive sensitivity adults s5 2020_2021 sensitive sensitivity season5_start_date @@ -21819,7 +14856,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2021_2022_sensitive_sensitivity.csv + csv: output/input_processed_adults_2021_2022_sensitive_sensitivity.csv describe_dataset_adults_s6_sensitive_sensitivity: run: r:latest analysis/report.R adults season6_start_date season6_end_date sensitive @@ -21840,16 +14877,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2021_2022_sensitive_*.csv - analyse_dataset_adults_rsv_further_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season6_start_date - season6_end_date sensitive sensitivity adults s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_adults_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2021_2022_sensitive_*.csv - analyse_dataset_adults_flu_s6_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season6_start_date season6_end_date sensitive sensitivity adults s6 2021_2022 sensitive sensitivity season6_start_date @@ -21919,7 +14946,7 @@ actions: - process_household_information_s7 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_adults_2022_2023_sensitive_sensitivity.csv + csv: output/input_processed_adults_2022_2023_sensitive_sensitivity.csv describe_dataset_adults_s7_sensitive_sensitivity: run: r:latest analysis/report.R adults season7_start_date season7_end_date sensitive @@ -21940,16 +14967,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_adults_2022_2023_sensitive_*.csv - analyse_dataset_adults_rsv_further_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R adults season7_start_date - season7_end_date sensitive sensitivity adults s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_adults_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_adults_2022_2023_sensitive_*.csv - analyse_dataset_adults_flu_s7_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R adults season7_start_date season7_end_date sensitive sensitivity adults s7 2022_2023 sensitive sensitivity season7_start_date @@ -22023,7 +15040,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2016_2017_sensitive_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2016_2017_sensitive_sensitivity.csv describe_dataset_children_and_adolescents_s1_sensitive_sensitivity: run: r:latest analysis/report.R children_and_adolescents season1_start_date season1_end_date @@ -22045,16 +15062,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2016_2017_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season1_start_date season1_end_date sensitive sensitivity children_and_adolescents - s1 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_children_and_adolescents_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2016_2017_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s1_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season1_start_date season1_end_date sensitive sensitivity children_and_adolescents s1 2016_2017 @@ -22106,7 +15113,7 @@ actions: - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2017_2018_sensitive_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2017_2018_sensitive_sensitivity.csv describe_dataset_children_and_adolescents_s2_sensitive_sensitivity: run: r:latest analysis/report.R children_and_adolescents season2_start_date season2_end_date @@ -22128,16 +15135,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2017_2018_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season2_start_date season2_end_date sensitive sensitivity children_and_adolescents - s2 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_children_and_adolescents_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2017_2018_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s2_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season2_start_date season2_end_date sensitive sensitivity children_and_adolescents s2 2017_2018 @@ -22189,7 +15186,7 @@ actions: - process_household_information_s3 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2018_2019_sensitive_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2018_2019_sensitive_sensitivity.csv describe_dataset_children_and_adolescents_s3_sensitive_sensitivity: run: r:latest analysis/report.R children_and_adolescents season3_start_date season3_end_date @@ -22211,16 +15208,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2018_2019_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season3_start_date season3_end_date sensitive sensitivity children_and_adolescents - s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_children_and_adolescents_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2018_2019_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s3_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season3_start_date season3_end_date sensitive sensitivity children_and_adolescents s3 2018_2019 @@ -22272,7 +15259,7 @@ actions: - process_household_information_s4 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2019_2020_sensitive_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2019_2020_sensitive_sensitivity.csv describe_dataset_children_and_adolescents_s4_sensitive_sensitivity: run: r:latest analysis/report.R children_and_adolescents season4_start_date season4_end_date @@ -22294,16 +15281,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2019_2020_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season4_start_date season4_end_date sensitive sensitivity children_and_adolescents - s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_children_and_adolescents_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2019_2020_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s4_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season4_start_date season4_end_date sensitive sensitivity children_and_adolescents s4 2019_2020 @@ -22375,7 +15352,7 @@ actions: - process_household_information_s5 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2020_2021_sensitive_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2020_2021_sensitive_sensitivity.csv describe_dataset_children_and_adolescents_s5_sensitive_sensitivity: run: r:latest analysis/report.R children_and_adolescents season5_start_date season5_end_date @@ -22397,16 +15374,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2020_2021_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season5_start_date season5_end_date sensitive sensitivity children_and_adolescents - s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_children_and_adolescents_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2020_2021_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s5_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season5_start_date season5_end_date sensitive sensitivity children_and_adolescents s5 2020_2021 @@ -22478,7 +15445,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2021_2022_sensitive_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2021_2022_sensitive_sensitivity.csv describe_dataset_children_and_adolescents_s6_sensitive_sensitivity: run: r:latest analysis/report.R children_and_adolescents season6_start_date season6_end_date @@ -22500,16 +15467,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2021_2022_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season6_start_date season6_end_date sensitive sensitivity children_and_adolescents - s6 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_children_and_adolescents_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2021_2022_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s6_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season6_start_date season6_end_date sensitive sensitivity children_and_adolescents s6 2021_2022 @@ -22581,7 +15538,7 @@ actions: - process_household_information_s7 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_children_and_adolescents_2022_2023_sensitive_sensitivity.csv + csv: output/input_processed_children_and_adolescents_2022_2023_sensitive_sensitivity.csv describe_dataset_children_and_adolescents_s7_sensitive_sensitivity: run: r:latest analysis/report.R children_and_adolescents season7_start_date season7_end_date @@ -22603,16 +15560,6 @@ actions: moderately_sensitive: csv: output/results/models/rsv_sensitivity/*_children_and_adolescents_2022_2023_sensitive_*.csv - analyse_dataset_children_and_adolescents_rsv_further_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_models.R children_and_adolescents - season7_start_date season7_end_date sensitive sensitivity children_and_adolescents - s7 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_children_and_adolescents_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_sensitivity/further_*_children_and_adolescents_2022_2023_sensitive_*.csv - analyse_dataset_children_and_adolescents_flu_s7_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_models.R children_and_adolescents season7_start_date season7_end_date sensitive sensitivity children_and_adolescents s7 2022_2023 @@ -22688,7 +15635,7 @@ actions: - process_household_information_s1 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2016_2017_sensitive_sensitivity.csv + csv: output/input_processed_infants_2016_2017_sensitive_sensitivity.csv describe_dataset_infants_s1_sensitive_sensitivity: run: r:latest analysis/report.R infants season1_start_date season1_end_date sensitive @@ -22909,216 +15856,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season1_start_date season1_end_date sensitive sensitivity infants s1 - 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season1_start_date season1_end_date sensitive sensitivity infants s1 - 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season1_start_date season1_end_date sensitive sensitivity infants s1 - 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season1_start_date season1_end_date sensitive sensitivity infants s1 2016_2017 - sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season1_start_date season1_end_date sensitive sensitivity infants s1 2016_2017 - sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season1_start_date season1_end_date sensitive sensitivity infants s1 - 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date sensitive sensitivity infants s1 2016_2017 - sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season1_start_date season1_end_date sensitive sensitivity infants s1 2016_2017 - sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season1_start_date season1_end_date sensitive sensitivity infants s1 - 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season1_start_date season1_end_date sensitive sensitivity infants s1 - 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season1_start_date - season1_end_date sensitive sensitivity infants s1 2016_2017 sensitive sensitivity - season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s1_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season1_start_date season1_end_date sensitive sensitivity infants s1 - 2016_2017 sensitive sensitivity season1_start_date season1_end_date - needs: - - process_dataset_infants_s1_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2016_2017_sensitive_sensitivity.csv - process_dataset_infants_s2_sensitive_sensitivity: run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season2_start_date season2_end_date sensitive primary sensitivity infants s2 2017_2018 season2_start_date @@ -23128,7 +15865,7 @@ actions: - process_household_information_s2 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2017_2018_sensitive_sensitivity.csv + csv: output/input_processed_infants_2017_2018_sensitive_sensitivity.csv describe_dataset_infants_s2_sensitive_sensitivity: run: r:latest analysis/report.R infants season2_start_date season2_end_date sensitive @@ -23349,655 +16086,235 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season2_start_date season2_end_date sensitive sensitivity infants s2 - 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season2_start_date season2_end_date sensitive sensitivity infants s2 - 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_hh_comp_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s2_sensitive_sensitivity: - 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 sensitive sensitivity infants s2 - 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season2_start_date season2_end_date sensitive sensitivity infants s2 2017_2018 - sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season2_start_date season2_end_date sensitive sensitivity infants s2 2017_2018 - sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s2_sensitive_sensitivity: - 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 sensitive sensitivity infants s2 - 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date sensitive sensitivity infants s2 2017_2018 - sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season2_start_date season2_end_date sensitive sensitivity infants s2 2017_2018 - sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s2_sensitive_sensitivity: - 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 sensitive sensitivity infants s2 - 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s2_sensitive_sensitivity: - 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 sensitive sensitivity infants s2 - 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season2_start_date - season2_end_date sensitive sensitivity infants s2 2017_2018 sensitive sensitivity - season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s2_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season2_start_date season2_end_date sensitive sensitivity infants s2 - 2017_2018 sensitive sensitivity season2_start_date season2_end_date - needs: - - process_dataset_infants_s2_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2017_2018_sensitive_sensitivity.csv - - process_dataset_infants_s3_sensitive_sensitivity: - run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season3_start_date - season3_end_date sensitive primary sensitivity infants s3 2018_2019 season3_start_date - season3_end_date sensitive primary sensitivity + process_dataset_infants_s3_sensitive_sensitivity: + run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season3_start_date + season3_end_date sensitive primary sensitivity infants s3 2018_2019 season3_start_date + season3_end_date sensitive primary sensitivity needs: - generate_dataset_infants_s3_sensitive_primary - - process_household_information_s3 - outputs: - moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2018_2019_sensitive_sensitivity.csv - - describe_dataset_infants_s3_sensitive_sensitivity: - run: r:latest analysis/report.R infants season3_start_date season3_end_date sensitive - sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/rates/rates_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R - infants season3_start_date season3_end_date sensitive sensitivity infants s3 - 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R - infants season3_start_date season3_end_date sensitive sensitivity infants s3 - 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_hh_comp_models.R - infants season3_start_date season3_end_date sensitive sensitivity infants s3 - 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R - infants season3_start_date season3_end_date sensitive sensitivity infants s3 - 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_hh_comp_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_hh_comp_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_sensitivity: - 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 sensitive sensitivity infants s3 - 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ses_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ses_hh_comp_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ses_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ses_hh_comp_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_sensitive_sensitivity: - 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 sensitive sensitivity infants s3 - 2018_2019 sensitive sensitivity season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_full_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_full_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_full_models.R infants season3_start_date - season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity - season3_start_date season3_end_date - needs: - - process_dataset_infants_s3_sensitive_sensitivity + - process_household_information_s3 outputs: moderately_sensitive: - csv: output/results/models/flu_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/input_processed_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_overall_and_all_cause_full_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R - infants season3_start_date season3_end_date sensitive sensitivity infants s3 - 2018_2019 sensitive sensitivity season3_start_date season3_end_date + describe_dataset_infants_s3_sensitive_sensitivity: + run: r:latest analysis/report.R infants season3_start_date season3_end_date sensitive + sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/rates/rates_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season3_start_date + analyse_dataset_infants_rsv_ethnicity_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/rsv_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season3_start_date + analyse_dataset_infants_flu_ethnicity_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/flu_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R + analyse_dataset_infants_overall_and_all_cause_ethnicity_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season3_start_date + analyse_dataset_infants_rsv_ses_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ses_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/rsv_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season3_start_date + analyse_dataset_infants_flu_ses_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ses_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/flu_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R + analyse_dataset_infants_overall_and_all_cause_ses_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season3_start_date + analyse_dataset_infants_rsv_hh_comp_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_hh_comp_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/rsv_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season3_start_date + analyse_dataset_infants_flu_hh_comp_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_hh_comp_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/flu_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R + analyse_dataset_infants_overall_and_all_cause_hh_comp_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_hh_comp_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 - sensitive sensitivity season3_start_date season3_end_date + analyse_dataset_infants_rsv_ethnicity_ses_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season3_start_date + season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity + season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 - sensitive sensitivity season3_start_date season3_end_date + analyse_dataset_infants_flu_ethnicity_ses_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants season3_start_date + season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity + season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 - sensitive sensitivity season3_start_date season3_end_date + analyse_dataset_infants_rsv_ethnicity_hh_comp_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity + season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 - sensitive sensitivity season3_start_date season3_end_date + analyse_dataset_infants_flu_ethnicity_hh_comp_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_hh_comp_models.R infants season3_start_date + season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity + season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s3_sensitive_sensitivity: + 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 sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season3_start_date + analyse_dataset_infants_rsv_ses_hh_comp_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ses_hh_comp_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ses_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season3_start_date + analyse_dataset_infants_flu_ses_hh_comp_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ses_hh_comp_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s3_sensitive_sensitivity: + 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 sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_full_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season3_start_date + analyse_dataset_infants_rsv_full_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/rsv_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_full_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season3_start_date + analyse_dataset_infants_flu_full_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_full_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/flu_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_full_s3_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R + analyse_dataset_infants_overall_and_all_cause_full_s3_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R infants season3_start_date season3_end_date sensitive sensitivity infants s3 2018_2019 sensitive sensitivity season3_start_date season3_end_date needs: - process_dataset_infants_s3_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2018_2019_sensitive_sensitivity.csv process_dataset_infants_s4_sensitive_sensitivity: run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season4_start_date @@ -24008,7 +16325,7 @@ actions: - process_household_information_s4 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2019_2020_sensitive_sensitivity.csv + csv: output/input_processed_infants_2019_2020_sensitive_sensitivity.csv describe_dataset_infants_s4_sensitive_sensitivity: run: r:latest analysis/report.R infants season4_start_date season4_end_date sensitive @@ -24152,292 +16469,82 @@ actions: analyse_dataset_infants_flu_ethnicity_hh_comp_s4_sensitive_sensitivity: run: r:latest analysis/outcome_flu/flu_ethnicity_hh_comp_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ses_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ses_hh_comp_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ses_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ses_hh_comp_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_hh_comp_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_full_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_full_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_full_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_full_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 - sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 - sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 - sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 - sensitive sensitivity season4_start_date season4_end_date + season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s4_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_hh_comp_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_rsv_ses_hh_comp_s4_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ses_hh_comp_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ses_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season4_start_date + analyse_dataset_infants_flu_ses_hh_comp_s4_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ses_hh_comp_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s4_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_hh_comp_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_full_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season4_start_date + analyse_dataset_infants_rsv_full_s4_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/rsv_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_full_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season4_start_date + analyse_dataset_infants_flu_full_s4_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_full_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/flu_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_full_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R + analyse_dataset_infants_overall_and_all_cause_full_s4_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R infants season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity season4_start_date season4_end_date needs: - process_dataset_infants_s4_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv analyse_dataset_infants_covid_ethnicity_s4_sensitive_sensitivity: run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season4_start_date @@ -24509,76 +16616,6 @@ actions: moderately_sensitive: csv: output/results/models/covid_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - analyse_dataset_infants_further_covid_ethnicity_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 - sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 - sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season4_start_date season4_end_date sensitive sensitivity infants s4 - 2019_2020 sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season4_start_date season4_end_date sensitive sensitivity infants s4 2019_2020 - sensitive sensitivity season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s4_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season4_start_date - season4_end_date sensitive sensitivity infants s4 2019_2020 sensitive sensitivity - season4_start_date season4_end_date - needs: - - process_dataset_infants_s4_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2019_2020_sensitive_sensitivity.csv - process_dataset_infants_s5_sensitive_sensitivity: run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season5_start_date season5_end_date sensitive primary sensitivity infants s5 2020_2021 season5_start_date @@ -24588,7 +16625,7 @@ actions: - process_household_information_s5 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2020_2021_sensitive_sensitivity.csv + csv: output/input_processed_infants_2020_2021_sensitive_sensitivity.csv describe_dataset_infants_s5_sensitive_sensitivity: run: r:latest analysis/report.R infants season5_start_date season5_end_date sensitive @@ -24690,334 +16727,124 @@ actions: csv: output/results/models/overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv analyse_dataset_infants_rsv_ethnicity_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R - infants season5_start_date season5_end_date sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ethnicity_hh_comp_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ethnicity_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ethnicity_hh_comp_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_sensitivity: - 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 sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_ses_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_ses_hh_comp_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_ses_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_ses_hh_comp_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_sensitive_sensitivity: - 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 sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_full_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_full_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_full_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_full_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R - infants season5_start_date season5_end_date sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season5_start_date season5_end_date sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season5_start_date season5_end_date sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s5_sensitive_sensitivity: - 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 sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 - sensitive sensitivity season5_start_date season5_end_date + run: r:latest analysis/outcome_rsv/rsv_ethnicity_ses_models.R infants season5_start_date + season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity + season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/rsv_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 - sensitive sensitivity season5_start_date season5_end_date + analyse_dataset_infants_flu_ethnicity_ses_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_ses_models.R infants season5_start_date + season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity + season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/flu_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R + analyse_dataset_infants_overall_and_all_cause_ethnicity_ses_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ethnicity_ses_models.R infants season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 - sensitive sensitivity season5_start_date season5_end_date + analyse_dataset_infants_rsv_ethnicity_hh_comp_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity + season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/rsv_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 - sensitive sensitivity season5_start_date season5_end_date + analyse_dataset_infants_flu_ethnicity_hh_comp_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ethnicity_hh_comp_models.R infants season5_start_date + season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity + season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/flu_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R + analyse_dataset_infants_overall_and_all_cause_ethnicity_hh_comp_s5_sensitive_sensitivity: + 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 sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ses_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season5_start_date + analyse_dataset_infants_rsv_ses_hh_comp_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_ses_hh_comp_models.R infants season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/rsv_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_ses_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season5_start_date + analyse_dataset_infants_flu_ses_hh_comp_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_ses_hh_comp_models.R infants season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R + analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s5_sensitive_sensitivity: + 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 sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_full_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season5_start_date + analyse_dataset_infants_rsv_full_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/rsv_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_full_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season5_start_date + analyse_dataset_infants_flu_full_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_full_models.R infants season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/flu_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_full_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R + analyse_dataset_infants_overall_and_all_cause_full_s5_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R infants season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity season5_start_date season5_end_date needs: - process_dataset_infants_s5_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv analyse_dataset_infants_covid_ethnicity_s5_sensitive_sensitivity: run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season5_start_date @@ -25089,76 +16916,6 @@ actions: moderately_sensitive: csv: output/results/models/covid_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - analyse_dataset_infants_further_covid_ethnicity_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 - sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 - sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season5_start_date season5_end_date sensitive sensitivity infants s5 - 2020_2021 sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season5_start_date season5_end_date sensitive sensitivity infants s5 2020_2021 - sensitive sensitivity season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s5_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season5_start_date - season5_end_date sensitive sensitivity infants s5 2020_2021 sensitive sensitivity - season5_start_date season5_end_date - needs: - - process_dataset_infants_s5_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2020_2021_sensitive_sensitivity.csv - process_dataset_infants_s6_sensitive_sensitivity: run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season6_start_date season6_end_date sensitive primary sensitivity infants s6 2021_2022 season6_start_date @@ -25168,7 +16925,7 @@ actions: - process_household_information_s6 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2021_2022_sensitive_sensitivity.csv + csv: output/input_processed_infants_2021_2022_sensitive_sensitivity.csv describe_dataset_infants_s6_sensitive_sensitivity: run: r:latest analysis/report.R infants season6_start_date season6_end_date sensitive @@ -25350,254 +17107,44 @@ actions: csv: output/results/models/flu_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv analyse_dataset_infants_overall_and_all_cause_ses_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_hh_comp_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_rsv_full_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/rsv_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_flu_full_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/flu_full_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/flu_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_overall_and_all_cause_full_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 - sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 - sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 - sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 - sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_ses_hh_comp_models.R infants season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_full_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season6_start_date + analyse_dataset_infants_rsv_full_s6_sensitive_sensitivity: + run: r:latest analysis/outcome_rsv/rsv_full_models.R infants season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv + csv: output/results/models/rsv_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - analyse_dataset_infants_further_flu_full_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season6_start_date + analyse_dataset_infants_flu_full_s6_sensitive_sensitivity: + run: r:latest analysis/outcome_flu/flu_full_models.R infants season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv + csv: output/results/models/flu_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - analyse_dataset_infants_further_overall_and_all_cause_full_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R + analyse_dataset_infants_overall_and_all_cause_full_s6_sensitive_sensitivity: + run: r:latest analysis/outcome_overall_and_all_cause/overall_and_all_cause_full_models.R infants season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity season6_start_date season6_end_date needs: - process_dataset_infants_s6_sensitive_sensitivity outputs: moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv + csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv analyse_dataset_infants_covid_ethnicity_s6_sensitive_sensitivity: run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season6_start_date @@ -25669,76 +17216,6 @@ actions: moderately_sensitive: csv: output/results/models/covid_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - analyse_dataset_infants_further_covid_ethnicity_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 - sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 - sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season6_start_date season6_end_date sensitive sensitivity infants s6 - 2021_2022 sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season6_start_date season6_end_date sensitive sensitivity infants s6 2021_2022 - sensitive sensitivity season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s6_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season6_start_date - season6_end_date sensitive sensitivity infants s6 2021_2022 sensitive sensitivity - season6_start_date season6_end_date - needs: - - process_dataset_infants_s6_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2021_2022_sensitive_sensitivity.csv - process_dataset_infants_s7_sensitive_sensitivity: run: r:latest analysis/sensitivity_analyses/data_processing_sens.R infants season7_start_date season7_end_date sensitive primary sensitivity infants s7 2022_2023 season7_start_date @@ -25748,7 +17225,7 @@ actions: - process_household_information_s7 outputs: moderately_sensitive: - csv: output/sensitivity/input_processed_infants_2022_2023_sensitive_sensitivity.csv + csv: output/input_processed_infants_2022_2023_sensitive_sensitivity.csv describe_dataset_infants_s7_sensitive_sensitivity: run: r:latest analysis/report.R infants season7_start_date season7_end_date sensitive @@ -25969,216 +17446,6 @@ actions: moderately_sensitive: csv: output/results/models/overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - analyse_dataset_infants_further_rsv_ethnicity_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_hh_comp_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_hh_comp_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_hh_comp_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_ses_models.R infants - season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 - sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_ses_models.R infants - season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 - sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_ses_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ethnicity_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 - sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ethnicity_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ethnicity_hh_comp_models.R infants - season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 - sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ethnicity_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_ses_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_ses_hh_comp_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_ses_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_ses_hh_comp_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_ses_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_ses_hh_comp_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_rsv_full_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_rsv/further_rsv_full_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_rsv_full_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_flu_full_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_flu/further_flu_full_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_flu_full_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_overall_and_all_cause_full_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_overall_and_all_cause/further_overall_and_all_cause_full_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_overall_and_all_cause_full_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - analyse_dataset_infants_covid_ethnicity_s7_sensitive_sensitivity: run: r:latest analysis/outcome_covid/covid_ethnicity_models.R infants season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity @@ -26249,76 +17516,6 @@ actions: moderately_sensitive: csv: output/results/models/covid_full_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - analyse_dataset_infants_further_covid_ethnicity_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_models.R infants - season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 - sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infantsfurther__covid_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_hh_comp_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_ses_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_ses_models.R infants - season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 - sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_ses_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ethnicity_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ethnicity_hh_comp_models.R - infants season7_start_date season7_end_date sensitive sensitivity infants s7 - 2022_2023 sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ethnicity_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_ses_hh_comp_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_ses_hh_comp_models.R infants - season7_start_date season7_end_date sensitive sensitivity infants s7 2022_2023 - sensitive sensitivity season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_ses_hh_comp_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - - analyse_dataset_infants_further_covid_full_s7_sensitive_sensitivity: - run: r:latest analysis/outcome_covid/further_covid_full_models.R infants season7_start_date - season7_end_date sensitive sensitivity infants s7 2022_2023 sensitive sensitivity - season7_start_date season7_end_date - needs: - - process_dataset_infants_s7_sensitive_sensitivity - outputs: - moderately_sensitive: - csv: output/results/models/further_covid_full_model_outputs_infants_2022_2023_sensitive_sensitivity.csv - ## # # # # # # # # # # # # # # # # # # # ## Files for release ## # # # # # # # # # # # # # # # # # # #