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Job request: 5324

Organisation:
University of Bristol
Workspace:
covid-ve-change-over-time-main
ID:
2wyb3codke2drmd4
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Elsie Horne requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

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Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## #################################### 
  ## preliminaries 
  ## #################################### 

  design:
    run: r:latest analysis/design.R
    outputs:
      moderately_sensitive:
        study_dates_json: output/lib/study_parameters.json
        study_dates_rds: output/lib/study_parameters.rds
        jcvi_groups: output/lib/jcvi_groups.csv
        elig_dates: output/lib/elig_dates.csv
        regions: output/lib/regions.csv
        model_varlist: output/lib/model_varlist.rds
        outcomes: output/lib/outcomes.rds
        strata_vars: output/lib/strata_vars.rds
        subgroups: output/lib/subgroups.rds

  ## #################################### 
  ## study definition 
  ## #################################### 
  ## generate dummy data for study_definition 

  dummy_data:
    run: r:latest analysis/dummy_data.R
    needs:
    - design
    outputs:
      moderately_sensitive:
        dummy_data: analysis/dummy_data.feather

  ## study definition 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    dummy_data_file: analysis/dummy_data.feather
    needs:
    - design
    - dummy_data
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  ## #################################### 
  ## preprocessing 
  ## #################################### 
  ## process data from study_definition 

  data_input_process:
    run: r:latest analysis/preprocess/data_input_process.R
    needs:
    - design
    - dummy_data
    - generate_study_population
    outputs:
      highly_sensitive:
        data_wide_vax_dates: output/data/data_wide_vax_dates.rds
        data_long_shielded_dates: output/data/data_long_shielded_dates.rds
        data_long_nonshielded_dates: output/data/data_long_nonshielded_dates.rds
        data_long_bmi_dates: output/data/data_long_bmi_dates.rds
        data_processed: output/data/data_processed.rds
      moderately_sensitive:
        data_properties: output/tables/data_*_tabulate.txt

  ## apply eligiblity criteria from boxes a and b 

  data_eligible_ab:
    run: r:latest analysis/preprocess/data_eligible_ab.R
    needs:
    - design
    - data_input_process
    outputs:
      highly_sensitive:
        data_eligible_a: output/data/data_eligible_a.rds
        data_eligible_b: output/data/data_eligible_b.rds
      moderately_sensitive:
        eligibility_count: output/tables/eligibility_count_ab.txt
        group_age_ranges: output/lib/group_age_ranges.csv

  ## #################################### 
  ## second_vax_period 
  ## #################################### 
  ## identify second vaccination time periods 
  ## create dataset for identifying second vaccination time periods 

  data_2nd_vax_dates:
    run: r:latest analysis/second_vax_period/data_2nd_vax_dates.R
    needs:
    - design
    - data_input_process
    - data_eligible_ab
    outputs:
      highly_sensitive:
        data_vax_plot: output/second_vax_period/data/data_vax_plot.rds
        second_vax_period_dates_rds: output/second_vax_period/data/second_vax_period_dates.rds
      moderately_sensitive:
        second_vax_period_dates_txt: output/second_vax_period/tables/second_vax_period_dates.txt

  ## plot second vaccination time periods 

  plot_2nd_vax_dates:
    run: r:latest analysis/second_vax_period/plot_2nd_vax_dates.R
    needs:
    - design
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      moderately_sensitive:
        plots_by_region: output/second_vax_period/images/plot_by_region_*.png

  ## apply eligiblity criteria from boxes c, d and e 

  data_eligible_cde:
    run: r:latest analysis/second_vax_period/data_eligible_cde.R
    needs:
    - design
    - data_input_process
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      highly_sensitive:
        data_eligible_e_vax: output/data/data_eligible_e_vax.rds
        data_eligible_e_unvax: output/data/data_eligible_e_unvax.rds
        data_eligible_e: output/data/data_eligible_e.csv

  ## #################################### 
  ## study definition tests 
  ## #################################### 
  ## generate dummy data for study_definition_tests 

  dummy_data_tests:
    run: r:latest analysis/dummy_data_tests.R
    needs:
    - design
    - dummy_data
    - data_eligible_cde
    outputs:
      moderately_sensitive:
        dummy_data_tests: analysis/dummy_data_tests.feather

  ## study definition tests 

  generate_covid_tests_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tests
      --output-format feather
    dummy_data_file: analysis/dummy_data_tests.feather
    needs:
    - design
    - data_eligible_cde
    - dummy_data_tests
    outputs:
      highly_sensitive:
        cohort: output/input_tests.feather

  ## check the tests data as expected and save processed data 

  process_tests:
    run: r:latest analysis/tests/process_tests.R
    needs:
    - design
    - data_input_process
    - data_eligible_cde
    - generate_covid_tests_data
    outputs:
      highly_sensitive:
        data_tests: output/data/data_tests.rds
        data_pregnancy: output/data/data_pregnancy.rds
        data_age: output/data/data_age.rds
      moderately_sensitive:
        pos_rate_distribution: output/tests/images/pos_rate_distribution.png

  ## #################################### 
  ## subsequent vaccination 
  ## #################################### 
  ## plot cumulative incidence of subsequent vaccination 

  plot_cumulative_incidence:
    run: r:latest analysis/subsequent_vax/plot_cumulative_incidence.R
    needs:
    - design
    - data_input_process
    - data_eligible_cde
    outputs:
      moderately_sensitive:
        ci_vax: output/subsequent_vax/images/ci_vax_*.png
        survtable: output/subsequent_vax/tables/survtable_*.txt

  ## #################################### 
  ## table 1 for report 
  ## #################################### 
  ## create table 1 for all and for each subgroup 

  table1:
    run: r:latest analysis/report/table1.R
    needs:
    - design
    - data_input_process
    - data_eligible_cde
    - process_tests
    outputs:
      moderately_sensitive:
        table_csv: output/report/tables/table1_*_REDACTED.csv
        table_html: output/report/tables/table1_*_REDACTED.html

  ## #################################### 
  ## comparisons 
  ## #################################### 
  ## process comparisons data 

  data_comparisons_process:
    run: r:latest analysis/comparisons/data_comparisons_process.R
    needs:
    - design
    - data_input_process
    - data_2nd_vax_dates
    - data_eligible_cde
    - process_tests
    outputs:
      highly_sensitive:
        data_comparisons: output/comparisons/data/data_comparisons_*.rds

  ## process tte data 

  data_tte_process_BNT162b2:
    run: r:latest analysis/comparisons/data_tte_process.R BNT162b2
    needs:
    - design
    - data_input_process
    - data_comparisons_process
    - process_tests
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/tte/data/data_tte_BNT162b2*.rds
        event_counts: output/tte/tables/event_counts_BNT162b2.rds

  data_tte_process_ChAdOx:
    run: r:latest analysis/comparisons/data_tte_process.R ChAdOx
    needs:
    - design
    - data_input_process
    - data_comparisons_process
    - process_tests
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/tte/data/data_tte_ChAdOx*.rds
        event_counts: output/tte/tables/event_counts_ChAdOx.rds

  data_tte_process_both:
    run: r:latest analysis/comparisons/data_tte_process.R both
    needs:
    - design
    - data_input_process
    - data_comparisons_process
    - process_tests
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/tte/data/data_tte_both*.rds
        event_counts: output/tte/tables/event_counts_both.rds

  ## process event counts tables 

  process_event_count_tables:
    run: r:latest analysis/comparisons/process_event_count_tables.R
    needs:
    - design
    - data_tte_process_BNT162b2
    - data_tte_process_ChAdOx
    outputs:
      moderately_sensitive:
        tidy_tables_events: output/tte/tables/tidy_events*.txt

  ## apply models 
  ## BNT162b2; 16-64 years and clinically vulnerable; anytest 
  ## preflight checks 

  preflight_BNT162b2_1_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_anytest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_1_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 anytest
    needs:
    - design
    - preflight_BNT162b2_1_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_anytest.rds

  ## BNT162b2; 16-64 years and clinically vulnerable; postest 
  ## preflight checks 

  preflight_BNT162b2_1_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_postest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_1_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 postest
    needs:
    - design
    - preflight_BNT162b2_1_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_postest.rds

  ## BNT162b2; 16-64 years and clinically vulnerable; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_1_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_1_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 covidadmitted
    needs:
    - design
    - preflight_BNT162b2_1_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_covidadmitted.rds

  ## BNT162b2; 16-64 years and clinically vulnerable; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_1_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_coviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_1_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 coviddeath
    needs:
    - design
    - preflight_BNT162b2_1_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_coviddeath.rds

  ## BNT162b2; 16-64 years and clinically vulnerable; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_1_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_1_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 noncoviddeath
    needs:
    - design
    - preflight_BNT162b2_1_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_BNT162b2_1:
    run: r:latest analysis/comparisons/tables_cox.R BNT162b2 1
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_BNT162b2
    - apply_model_cox_BNT162b2_1_anytest
    - apply_model_cox_BNT162b2_1_postest
    - apply_model_cox_BNT162b2_1_covidadmitted
    - apply_model_cox_BNT162b2_1_coviddeath
    - apply_model_cox_BNT162b2_1_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_1.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_1.txt

  ## BNT162b2; 18-39 years; anytest 
  ## preflight checks 

  preflight_BNT162b2_2_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_anytest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_2_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 anytest
    needs:
    - design
    - preflight_BNT162b2_2_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_anytest.rds

  ## BNT162b2; 18-39 years; postest 
  ## preflight checks 

  preflight_BNT162b2_2_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_postest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_2_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 postest
    needs:
    - design
    - preflight_BNT162b2_2_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_postest.rds

  ## BNT162b2; 18-39 years; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_2_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_2_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 covidadmitted
    needs:
    - design
    - preflight_BNT162b2_2_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_covidadmitted.rds

  ## BNT162b2; 18-39 years; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_2_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_coviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_2_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 coviddeath
    needs:
    - design
    - preflight_BNT162b2_2_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_coviddeath.rds

  ## BNT162b2; 18-39 years; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_2_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_2_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 noncoviddeath
    needs:
    - design
    - preflight_BNT162b2_2_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_BNT162b2_2:
    run: r:latest analysis/comparisons/tables_cox.R BNT162b2 2
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_BNT162b2
    - apply_model_cox_BNT162b2_2_anytest
    - apply_model_cox_BNT162b2_2_postest
    - apply_model_cox_BNT162b2_2_covidadmitted
    - apply_model_cox_BNT162b2_2_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_2.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_2.txt

  ## BNT162b2; 40-64 years; anytest 
  ## preflight checks 

  preflight_BNT162b2_3_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_anytest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_3_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 anytest
    needs:
    - design
    - preflight_BNT162b2_3_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_anytest.rds

  ## BNT162b2; 40-64 years; postest 
  ## preflight checks 

  preflight_BNT162b2_3_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_postest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_3_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 postest
    needs:
    - design
    - preflight_BNT162b2_3_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_postest.rds

  ## BNT162b2; 40-64 years; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_3_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_3_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 covidadmitted
    needs:
    - design
    - preflight_BNT162b2_3_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_covidadmitted.rds

  ## BNT162b2; 40-64 years; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_3_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_coviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_3_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 coviddeath
    needs:
    - design
    - preflight_BNT162b2_3_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_coviddeath.rds

  ## BNT162b2; 40-64 years; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_3_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_3_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 noncoviddeath
    needs:
    - design
    - preflight_BNT162b2_3_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_BNT162b2_3:
    run: r:latest analysis/comparisons/tables_cox.R BNT162b2 3
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_BNT162b2
    - apply_model_cox_BNT162b2_3_anytest
    - apply_model_cox_BNT162b2_3_postest
    - apply_model_cox_BNT162b2_3_covidadmitted
    - apply_model_cox_BNT162b2_3_coviddeath
    - apply_model_cox_BNT162b2_3_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_3.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_3.txt

  ## BNT162b2; 65+ years; anytest 
  ## preflight checks 

  preflight_BNT162b2_4_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_anytest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_4_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 anytest
    needs:
    - design
    - preflight_BNT162b2_4_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_anytest.rds

  ## BNT162b2; 65+ years; postest 
  ## preflight checks 

  preflight_BNT162b2_4_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_postest.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_4_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 postest
    needs:
    - design
    - preflight_BNT162b2_4_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_postest.rds

  ## BNT162b2; 65+ years; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_4_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_4_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 covidadmitted
    needs:
    - design
    - preflight_BNT162b2_4_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_covidadmitted.rds

  ## BNT162b2; 65+ years; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_4_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_coviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_4_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 coviddeath
    needs:
    - design
    - preflight_BNT162b2_4_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_coviddeath.rds

  ## BNT162b2; 65+ years; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_4_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_4_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 noncoviddeath
    needs:
    - design
    - preflight_BNT162b2_4_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_BNT162b2_4:
    run: r:latest analysis/comparisons/tables_cox.R BNT162b2 4
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_BNT162b2
    - apply_model_cox_BNT162b2_4_anytest
    - apply_model_cox_BNT162b2_4_postest
    - apply_model_cox_BNT162b2_4_covidadmitted
    - apply_model_cox_BNT162b2_4_coviddeath
    - apply_model_cox_BNT162b2_4_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_4.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_4.txt

  ## ChAdOx; 16-64 years and clinically vulnerable; anytest 
  ## preflight checks 

  preflight_ChAdOx_1_anytest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 1 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_1_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_anytest.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_1_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 anytest
    needs:
    - design
    - preflight_ChAdOx_1_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_1_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_anytest.rds

  ## ChAdOx; 16-64 years and clinically vulnerable; postest 
  ## preflight checks 

  preflight_ChAdOx_1_postest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 1 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_1_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_postest.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_1_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 postest
    needs:
    - design
    - preflight_ChAdOx_1_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_1_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_postest.rds

  ## ChAdOx; 16-64 years and clinically vulnerable; covidadmitted 
  ## preflight checks 

  preflight_ChAdOx_1_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 1 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_1_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_1_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 covidadmitted
    needs:
    - design
    - preflight_ChAdOx_1_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_1_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_covidadmitted.rds

  ## ChAdOx; 16-64 years and clinically vulnerable; coviddeath 
  ## preflight checks 

  preflight_ChAdOx_1_coviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 1 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_1_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_coviddeath.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_1_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 coviddeath
    needs:
    - design
    - preflight_ChAdOx_1_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_1_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_coviddeath.rds

  ## ChAdOx; 16-64 years and clinically vulnerable; noncoviddeath 
  ## preflight checks 

  preflight_ChAdOx_1_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 1 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_1_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_1_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 noncoviddeath
    needs:
    - design
    - preflight_ChAdOx_1_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_1_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_ChAdOx_1:
    run: r:latest analysis/comparisons/tables_cox.R ChAdOx 1
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_ChAdOx
    - apply_model_cox_ChAdOx_1_anytest
    - apply_model_cox_ChAdOx_1_postest
    - apply_model_cox_ChAdOx_1_covidadmitted
    - apply_model_cox_ChAdOx_1_coviddeath
    - apply_model_cox_ChAdOx_1_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_ChAdOx_1.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_ChAdOx_1.txt

  ## ChAdOx; 40-64 years; anytest 
  ## preflight checks 

  preflight_ChAdOx_3_anytest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 3 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_3_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_anytest.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_3_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 anytest
    needs:
    - design
    - preflight_ChAdOx_3_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_3_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_anytest.rds

  ## ChAdOx; 40-64 years; postest 
  ## preflight checks 

  preflight_ChAdOx_3_postest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 3 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_3_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_postest.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_3_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 postest
    needs:
    - design
    - preflight_ChAdOx_3_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_3_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_postest.rds

  ## ChAdOx; 40-64 years; covidadmitted 
  ## preflight checks 

  preflight_ChAdOx_3_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 3 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_3_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_3_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 covidadmitted
    needs:
    - design
    - preflight_ChAdOx_3_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_3_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_covidadmitted.rds

  ## ChAdOx; 40-64 years; coviddeath 
  ## preflight checks 

  preflight_ChAdOx_3_coviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 3 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_3_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_coviddeath.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_3_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 coviddeath
    needs:
    - design
    - preflight_ChAdOx_3_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_3_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_coviddeath.rds

  ## ChAdOx; 40-64 years; noncoviddeath 
  ## preflight checks 

  preflight_ChAdOx_3_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 3 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_3_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_3_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 noncoviddeath
    needs:
    - design
    - preflight_ChAdOx_3_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_3_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_ChAdOx_3:
    run: r:latest analysis/comparisons/tables_cox.R ChAdOx 3
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_ChAdOx
    - apply_model_cox_ChAdOx_3_anytest
    - apply_model_cox_ChAdOx_3_postest
    - apply_model_cox_ChAdOx_3_covidadmitted
    - apply_model_cox_ChAdOx_3_coviddeath
    - apply_model_cox_ChAdOx_3_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_ChAdOx_3.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_ChAdOx_3.txt

  ## ChAdOx; 65+ years; anytest 
  ## preflight checks 

  preflight_ChAdOx_4_anytest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 4 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_4_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_anytest.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_4_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 anytest
    needs:
    - design
    - preflight_ChAdOx_4_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_4_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_anytest.rds

  ## ChAdOx; 65+ years; postest 
  ## preflight checks 

  preflight_ChAdOx_4_postest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 4 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_4_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_postest.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_4_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 postest
    needs:
    - design
    - preflight_ChAdOx_4_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_4_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_postest.rds

  ## ChAdOx; 65+ years; covidadmitted 
  ## preflight checks 

  preflight_ChAdOx_4_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 4 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_4_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_4_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 covidadmitted
    needs:
    - design
    - preflight_ChAdOx_4_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_4_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_covidadmitted.rds

  ## ChAdOx; 65+ years; coviddeath 
  ## preflight checks 

  preflight_ChAdOx_4_coviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 4 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_4_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_coviddeath.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_4_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 coviddeath
    needs:
    - design
    - preflight_ChAdOx_4_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_4_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_coviddeath.rds

  ## ChAdOx; 65+ years; noncoviddeath 
  ## preflight checks 

  preflight_ChAdOx_4_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx 4 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx_4_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_ChAdOx_4_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 noncoviddeath
    needs:
    - design
    - preflight_ChAdOx_4_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_4_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_ChAdOx_4:
    run: r:latest analysis/comparisons/tables_cox.R ChAdOx 4
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_ChAdOx
    - apply_model_cox_ChAdOx_4_anytest
    - apply_model_cox_ChAdOx_4_postest
    - apply_model_cox_ChAdOx_4_covidadmitted
    - apply_model_cox_ChAdOx_4_coviddeath
    - apply_model_cox_ChAdOx_4_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_ChAdOx_4.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_ChAdOx_4.txt

  ## both; 16-64 years and clinically vulnerable; anytest 
  ## preflight checks 

  preflight_both_1_anytest:
    run: r:latest analysis/comparisons/preflight.R both 1 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_1_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_both_1_anytest.txt

  ## apply cox model 

  apply_model_cox_both_1_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 anytest
    needs:
    - design
    - preflight_both_1_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_both_1_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_both_1_anytest.rds

  ## both; 16-64 years and clinically vulnerable; postest 
  ## preflight checks 

  preflight_both_1_postest:
    run: r:latest analysis/comparisons/preflight.R both 1 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_1_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_both_1_postest.txt

  ## apply cox model 

  apply_model_cox_both_1_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 postest
    needs:
    - design
    - preflight_both_1_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_both_1_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_both_1_postest.rds

  ## both; 16-64 years and clinically vulnerable; covidadmitted 
  ## preflight checks 

  preflight_both_1_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R both 1 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_1_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_both_1_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_both_1_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 covidadmitted
    needs:
    - design
    - preflight_both_1_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_both_1_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_both_1_covidadmitted.rds

  ## both; 16-64 years and clinically vulnerable; coviddeath 
  ## preflight checks 

  preflight_both_1_coviddeath:
    run: r:latest analysis/comparisons/preflight.R both 1 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_1_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_both_1_coviddeath.txt

  ## apply cox model 

  apply_model_cox_both_1_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 coviddeath
    needs:
    - design
    - preflight_both_1_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_1_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_1_coviddeath.rds

  ## both; 16-64 years and clinically vulnerable; noncoviddeath 
  ## preflight checks 

  preflight_both_1_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R both 1 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_1_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_both_1_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_both_1_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 noncoviddeath
    needs:
    - design
    - preflight_both_1_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_1_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_1_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_both_1:
    run: r:latest analysis/comparisons/tables_cox.R both 1
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_both
    - apply_model_cox_both_1_anytest
    - apply_model_cox_both_1_postest
    - apply_model_cox_both_1_covidadmitted
    - apply_model_cox_both_1_coviddeath
    - apply_model_cox_both_1_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_both_1.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_both_1.txt

  ## both; 40-64 years; anytest 
  ## preflight checks 

  preflight_both_3_anytest:
    run: r:latest analysis/comparisons/preflight.R both 3 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_3_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_both_3_anytest.txt

  ## apply cox model 

  apply_model_cox_both_3_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 anytest
    needs:
    - design
    - preflight_both_3_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_both_3_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_both_3_anytest.rds

  ## both; 40-64 years; postest 
  ## preflight checks 

  preflight_both_3_postest:
    run: r:latest analysis/comparisons/preflight.R both 3 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_3_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_both_3_postest.txt

  ## apply cox model 

  apply_model_cox_both_3_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 postest
    needs:
    - design
    - preflight_both_3_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_both_3_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_both_3_postest.rds

  ## both; 40-64 years; covidadmitted 
  ## preflight checks 

  preflight_both_3_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R both 3 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_3_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_both_3_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_both_3_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 covidadmitted
    needs:
    - design
    - preflight_both_3_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_both_3_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_both_3_covidadmitted.rds

  ## both; 40-64 years; coviddeath 
  ## preflight checks 

  preflight_both_3_coviddeath:
    run: r:latest analysis/comparisons/preflight.R both 3 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_3_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_both_3_coviddeath.txt

  ## apply cox model 

  apply_model_cox_both_3_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 coviddeath
    needs:
    - design
    - preflight_both_3_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_3_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_3_coviddeath.rds

  ## both; 40-64 years; noncoviddeath 
  ## preflight checks 

  preflight_both_3_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R both 3 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_3_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_both_3_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_both_3_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 noncoviddeath
    needs:
    - design
    - preflight_both_3_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_3_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_3_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_both_3:
    run: r:latest analysis/comparisons/tables_cox.R both 3
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_both
    - apply_model_cox_both_3_anytest
    - apply_model_cox_both_3_postest
    - apply_model_cox_both_3_covidadmitted
    - apply_model_cox_both_3_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_both_3.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_both_3.txt

  ## both; 65+ years; anytest 
  ## preflight checks 

  preflight_both_4_anytest:
    run: r:latest analysis/comparisons/preflight.R both 4 anytest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_4_anytest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_4_anytest_*.html
        preflight_report: output/preflight/tables/preflight_report_both_4_anytest.txt

  ## apply cox model 

  apply_model_cox_both_4_anytest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 anytest
    needs:
    - design
    - preflight_both_4_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_4_anytest.rds
        model_summary: output/models_cox/data/modelcox_summary_both_4_anytest.rds
        model_glance: output/models_cox/data/modelcox_glance_both_4_anytest.rds

  ## both; 65+ years; postest 
  ## preflight checks 

  preflight_both_4_postest:
    run: r:latest analysis/comparisons/preflight.R both 4 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_4_postest.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_4_postest_*.html
        preflight_report: output/preflight/tables/preflight_report_both_4_postest.txt

  ## apply cox model 

  apply_model_cox_both_4_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 postest
    needs:
    - design
    - preflight_both_4_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_4_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_both_4_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_both_4_postest.rds

  ## both; 65+ years; covidadmitted 
  ## preflight checks 

  preflight_both_4_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R both 4 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_4_covidadmitted.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_4_covidadmitted_*.html
        preflight_report: output/preflight/tables/preflight_report_both_4_covidadmitted.txt

  ## apply cox model 

  apply_model_cox_both_4_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 covidadmitted
    needs:
    - design
    - preflight_both_4_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_4_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_both_4_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_both_4_covidadmitted.rds

  ## both; 65+ years; coviddeath 
  ## preflight checks 

  preflight_both_4_coviddeath:
    run: r:latest analysis/comparisons/preflight.R both 4 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_4_coviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_4_coviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_both_4_coviddeath.txt

  ## apply cox model 

  apply_model_cox_both_4_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 coviddeath
    needs:
    - design
    - preflight_both_4_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_4_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_4_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_4_coviddeath.rds

  ## both; 65+ years; noncoviddeath 
  ## preflight checks 

  preflight_both_4_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R both 4 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_4_noncoviddeath.rds
      moderately_sensitive:
        eventcheck_table: output/preflight/tables/eventcheck_both_4_noncoviddeath_*.html
        preflight_report: output/preflight/tables/preflight_report_both_4_noncoviddeath.txt

  ## apply cox model 

  apply_model_cox_both_4_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 noncoviddeath
    needs:
    - design
    - preflight_both_4_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_4_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_4_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_4_noncoviddeath.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_both_4:
    run: r:latest analysis/comparisons/tables_cox.R both 4
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_both
    - apply_model_cox_both_4_anytest
    - apply_model_cox_both_4_postest
    - apply_model_cox_both_4_covidadmitted
    - apply_model_cox_both_4_coviddeath
    - apply_model_cox_both_4_noncoviddeath
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_both_4.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_both_4.txt

  ## generate plots 
  ## plot anytest BNT162b2 

  plot_hr_anytest_BNT162b2:
    run: r:latest analysis/comparisons/plot_cox_anytest.R BNT162b2
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_BNT162b2_1_anytest
    - apply_model_cox_BNT162b2_2_anytest
    - apply_model_cox_BNT162b2_3_anytest
    - apply_model_cox_BNT162b2_4_anytest
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_anytest_BNT162b2_*.png

  ## plot other outcomes BNT162b2 

  plot_hr_BNT162b2:
    run: r:latest analysis/comparisons/plot_cox.R BNT162b2
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_BNT162b2_1_postest
    - apply_model_cox_BNT162b2_1_covidadmitted
    - apply_model_cox_BNT162b2_1_coviddeath
    - apply_model_cox_BNT162b2_1_noncoviddeath
    - apply_model_cox_BNT162b2_2_postest
    - apply_model_cox_BNT162b2_2_covidadmitted
    - apply_model_cox_BNT162b2_2_noncoviddeath
    - apply_model_cox_BNT162b2_3_postest
    - apply_model_cox_BNT162b2_3_covidadmitted
    - apply_model_cox_BNT162b2_3_coviddeath
    - apply_model_cox_BNT162b2_3_noncoviddeath
    - apply_model_cox_BNT162b2_4_postest
    - apply_model_cox_BNT162b2_4_covidadmitted
    - apply_model_cox_BNT162b2_4_coviddeath
    - apply_model_cox_BNT162b2_4_noncoviddeath
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_BNT162b2_*.png

  ## plot anytest ChAdOx 

  plot_hr_anytest_ChAdOx:
    run: r:latest analysis/comparisons/plot_cox_anytest.R ChAdOx
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_ChAdOx_1_anytest
    - apply_model_cox_ChAdOx_3_anytest
    - apply_model_cox_ChAdOx_4_anytest
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_anytest_ChAdOx_*.png

  ## plot other outcomes ChAdOx 

  plot_hr_ChAdOx:
    run: r:latest analysis/comparisons/plot_cox.R ChAdOx
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_ChAdOx_1_postest
    - apply_model_cox_ChAdOx_1_covidadmitted
    - apply_model_cox_ChAdOx_1_coviddeath
    - apply_model_cox_ChAdOx_1_noncoviddeath
    - apply_model_cox_ChAdOx_3_postest
    - apply_model_cox_ChAdOx_3_covidadmitted
    - apply_model_cox_ChAdOx_3_coviddeath
    - apply_model_cox_ChAdOx_3_noncoviddeath
    - apply_model_cox_ChAdOx_4_postest
    - apply_model_cox_ChAdOx_4_covidadmitted
    - apply_model_cox_ChAdOx_4_coviddeath
    - apply_model_cox_ChAdOx_4_noncoviddeath
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_ChAdOx_*.png

  ## plot anytest BNT162b2andChAdOx 

  plot_hr_anytest_BNT162b2andChAdOx:
    run: r:latest analysis/comparisons/plot_cox_anytest.R BNT162b2andChAdOx
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_BNT162b2_1_anytest
    - apply_model_cox_BNT162b2_3_anytest
    - apply_model_cox_BNT162b2_4_anytest
    - apply_model_cox_ChAdOx_1_anytest
    - apply_model_cox_ChAdOx_3_anytest
    - apply_model_cox_ChAdOx_4_anytest
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_anytest_BNT162b2andChAdOx_*.png

  ## plot other outcomes BNT162b2andChAdOx 

  plot_hr_BNT162b2andChAdOx:
    run: r:latest analysis/comparisons/plot_cox.R BNT162b2andChAdOx
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_BNT162b2_1_postest
    - apply_model_cox_BNT162b2_1_covidadmitted
    - apply_model_cox_BNT162b2_1_coviddeath
    - apply_model_cox_BNT162b2_1_noncoviddeath
    - apply_model_cox_BNT162b2_3_postest
    - apply_model_cox_BNT162b2_3_covidadmitted
    - apply_model_cox_BNT162b2_3_coviddeath
    - apply_model_cox_BNT162b2_3_noncoviddeath
    - apply_model_cox_BNT162b2_4_postest
    - apply_model_cox_BNT162b2_4_covidadmitted
    - apply_model_cox_BNT162b2_4_coviddeath
    - apply_model_cox_BNT162b2_4_noncoviddeath
    - apply_model_cox_ChAdOx_1_postest
    - apply_model_cox_ChAdOx_1_covidadmitted
    - apply_model_cox_ChAdOx_1_coviddeath
    - apply_model_cox_ChAdOx_1_noncoviddeath
    - apply_model_cox_ChAdOx_3_postest
    - apply_model_cox_ChAdOx_3_covidadmitted
    - apply_model_cox_ChAdOx_3_coviddeath
    - apply_model_cox_ChAdOx_3_noncoviddeath
    - apply_model_cox_ChAdOx_4_postest
    - apply_model_cox_ChAdOx_4_covidadmitted
    - apply_model_cox_ChAdOx_4_coviddeath
    - apply_model_cox_ChAdOx_4_noncoviddeath
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_BNT162b2andChAdOx_*.png

  ## plot anytest BNT162b2vsChAdOx 

  plot_hr_anytest_BNT162b2vsChAdOx:
    run: r:latest analysis/comparisons/plot_cox_anytest.R BNT162b2vsChAdOx
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_both_1_anytest
    - apply_model_cox_both_3_anytest
    - apply_model_cox_both_4_anytest
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_anytest_BNT162b2vsChAdOx_*.png

  ## plot other outcomes BNT162b2vsChAdOx 

  plot_hr_BNT162b2vsChAdOx:
    run: r:latest analysis/comparisons/plot_cox.R BNT162b2vsChAdOx
    needs:
    - design
    - data_2nd_vax_dates
    - apply_model_cox_both_1_postest
    - apply_model_cox_both_1_covidadmitted
    - apply_model_cox_both_1_coviddeath
    - apply_model_cox_both_1_noncoviddeath
    - apply_model_cox_both_3_postest
    - apply_model_cox_both_3_covidadmitted
    - apply_model_cox_both_3_noncoviddeath
    - apply_model_cox_both_4_postest
    - apply_model_cox_both_4_covidadmitted
    - apply_model_cox_both_4_coviddeath
    - apply_model_cox_both_4_noncoviddeath
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/hr_BNT162b2vsChAdOx_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 21:16:47

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-ve-change-over-time-main
Requested by
Elsie Horne
Branch
main
Force run dependencies
No
Git commit hash
bf4638e
Requested actions
  • preflight_both_1_anytest
  • apply_model_cox_both_1_anytest
  • preflight_both_1_postest
  • apply_model_cox_both_1_postest
  • preflight_both_1_covidadmitted
  • apply_model_cox_both_1_covidadmitted
  • preflight_both_1_coviddeath
  • apply_model_cox_both_1_coviddeath
  • preflight_both_1_noncoviddeath
  • apply_model_cox_both_1_noncoviddeath
  • tables_model_cox_both_1
  • preflight_both_3_anytest
  • apply_model_cox_both_3_anytest
  • preflight_both_3_postest
  • apply_model_cox_both_3_postest
  • preflight_both_3_covidadmitted
  • apply_model_cox_both_3_covidadmitted
  • preflight_both_3_coviddeath
  • apply_model_cox_both_3_coviddeath
  • preflight_both_3_noncoviddeath
  • apply_model_cox_both_3_noncoviddeath
  • tables_model_cox_both_3
  • preflight_both_4_anytest
  • apply_model_cox_both_4_anytest
  • preflight_both_4_postest
  • apply_model_cox_both_4_postest
  • preflight_both_4_covidadmitted
  • apply_model_cox_both_4_covidadmitted
  • preflight_both_4_coviddeath
  • apply_model_cox_both_4_coviddeath
  • preflight_both_4_noncoviddeath
  • apply_model_cox_both_4_noncoviddeath
  • tables_model_cox_both_4
  • plot_hr_anytest_BNT162b2
  • plot_hr_BNT162b2
  • plot_hr_anytest_ChAdOx
  • plot_hr_ChAdOx
  • plot_hr_anytest_BNT162b2andChAdOx
  • plot_hr_BNT162b2andChAdOx
  • plot_hr_anytest_BNT162b2vsChAdOx
  • plot_hr_BNT162b2vsChAdOx