project.yaml

version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml 
  ## This file is created by create_project.R 
  ## Edit and run create_project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## #################################### 
  ## study definition 
  ## #################################### 
  ## generate dummy data for study_definition 

  dummy_data_vax:
    run: r:latest analysis/dummy_data_vax.R
    outputs:
      moderately_sensitive:
        dummy_data: analysis/dummy_data_vax.feather

  ## study definition 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format feather
    dummy_data_file: analysis/dummy_data_vax.feather
    needs:
    - dummy_data_vax
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather

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

  data_input_process:
    run: r:latest analysis/preprocess/data_input_process.R
    needs:
    - dummy_data_vax
    - generate_study_population
    outputs:
      highly_sensitive:
        data_wide_vax_dates: output/data/data_wide_vax_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:
    - 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_ab: output/tables/eligibility_count_ab.csv
        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:
    - 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:
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      moderately_sensitive:
        plots_by_region: output/second_vax_period/images/plot_by_region_*.png
        plots_by_region_data: output/second_vax_period/images/plot_by_region_*.txt

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

  data_eligible_cde:
    run: r:latest analysis/preprocess/data_eligible_cde.R
    needs:
    - 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
      moderately_sensitive:
        eligibility_count_cde: output/tables/eligibility_count_cde.csv

  ## #################################### 
  ## study definition covs 
  ## #################################### 

  generate_covs_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covs
      --output-format feather
    needs:
    - data_eligible_cde
    outputs:
      highly_sensitive:
        cohort: output/input_covs.feather

  ## #################################### 
  ## process covariates data 
  ## #################################### 
  ## (includes anytest_date) 

  data_covariates_process:
    run: r:latest analysis/preprocess/data_covariates_process.R
    needs:
    - data_input_process
    - data_eligible_cde
    - generate_covs_data
    outputs:
      highly_sensitive:
        data_covariates: output/data/data_all.rds
      moderately_sensitive:
        data_min_max_fu_csv: output/lib/data_min_max_fu.csv

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

  plot_cumulative_incidence:
    run: r:latest analysis/subsequent_vax/plot_cumulative_incidence.R
    needs:
    - data_covariates_process
    outputs:
      moderately_sensitive:
        ci_vax: output/subsequent_vax/images/ci_vax.png
        survtable: output/subsequent_vax/tables/survtable_redacted.csv

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

  table1:
    run: r:latest analysis/report/table1.R
    needs:
    - data_eligible_ab
    - data_eligible_cde
    - data_covariates_process
    outputs:
      moderately_sensitive:
        eligibility_count_p1: output/tables/eligibility_count_p1.csv
        eligibility_count_all: output/tables/eligibility_count_all.csv
        table_csv: output/report/tables/table1_*_REDACTED.csv
        table_html: output/report/tables/table1_*_REDACTED.html

  ## #################################### 
  ## process time to event data 
  ## #################################### 
  ## process tte data 

  data_tte_process_BNT162b2:
    run: r:latest analysis/comparisons/data_tte_process.R BNT162b2
    needs:
    - data_covariates_process
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/tte/data/data_tte_BNT162b2*.rds
      moderately_sensitive:
        event_counts_csv: output/tte/data/event_counts_BNT162b2.csv
        event_counts_txt: output/tte/tables/event_counts_BNT162b2.txt

  data_tte_process_ChAdOx1:
    run: r:latest analysis/comparisons/data_tte_process.R ChAdOx1
    needs:
    - data_covariates_process
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/tte/data/data_tte_ChAdOx1*.rds
      moderately_sensitive:
        event_counts_csv: output/tte/data/event_counts_ChAdOx1.csv
        event_counts_txt: output/tte/tables/event_counts_ChAdOx1.txt

  data_tte_process_both:
    run: r:latest analysis/comparisons/data_tte_process.R both
    needs:
    - data_covariates_process
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/tte/data/data_tte_both*.rds
      moderately_sensitive:
        event_counts_csv: output/tte/data/event_counts_both.csv
        event_counts_txt: output/tte/tables/event_counts_both.txt

  ## check distribution of follow-up time in relation to variant dates 

  check_fu_1:
    run: r:latest analysis/comparisons/check_fu.R 1
    needs:
    - data_covariates_process
    outputs:
      moderately_sensitive:
        check_fu_plot: output/tte/images/check_fu_1.png
        check_fu_plot_data: output/tte/images/check_fu_1.csv

  check_fu_2:
    run: r:latest analysis/comparisons/check_fu.R 2
    needs:
    - data_covariates_process
    outputs:
      moderately_sensitive:
        check_fu_plot: output/tte/images/check_fu_2.png
        check_fu_plot_data: output/tte/images/check_fu_2.csv

  check_fu_3:
    run: r:latest analysis/comparisons/check_fu.R 3
    needs:
    - data_covariates_process
    outputs:
      moderately_sensitive:
        check_fu_plot: output/tte/images/check_fu_3.png
        check_fu_plot_data: output/tte/images/check_fu_3.csv

  check_fu_4:
    run: r:latest analysis/comparisons/check_fu.R 4
    needs:
    - data_covariates_process
    outputs:
      moderately_sensitive:
        check_fu_plot: output/tte/images/check_fu_4.png
        check_fu_plot_data: output/tte/images/check_fu_4.csv

  ## #################################### 
  ## apply models 
  ## #################################### 
  ## BNT162b2; 1; anytest 
  ## preflight checks 

  preflight_BNT162b2_1_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 anytest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_anytest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 1 anytest
    needs:
    - preflight_BNT162b2_1_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_anytest.txt

  ## BNT162b2; 1; postest 
  ## preflight checks 

  preflight_BNT162b2_1_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 postest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_postest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 1 postest
    needs:
    - preflight_BNT162b2_1_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_postest.txt

  ## BNT162b2; 1; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_1_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_covidadmitted*.rds
      moderately_sensitive:
        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_update.R BNT162b2 1 covidadmitted
    needs:
    - preflight_BNT162b2_1_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_covidadmitted.txt

  ## BNT162b2; 1; covidemergency 
  ## preflight checks 

  preflight_BNT162b2_1_covidemergency:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_1_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 covidemergency
    needs:
    - preflight_BNT162b2_1_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_covidemergency.txt

  ## BNT162b2; 1; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_1_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_coviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 1 coviddeath
    needs:
    - preflight_BNT162b2_1_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_coviddeath.txt

  ## BNT162b2; 1; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_1_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 1 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_1_noncoviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 1 noncoviddeath
    needs:
    - preflight_BNT162b2_1_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_noncoviddeath.txt

  ## BNT162b2; 2; anytest 
  ## preflight checks 

  preflight_BNT162b2_2_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 anytest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_anytest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 2 anytest
    needs:
    - preflight_BNT162b2_2_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_anytest.txt

  ## BNT162b2; 2; postest 
  ## preflight checks 

  preflight_BNT162b2_2_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 postest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_postest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 2 postest
    needs:
    - preflight_BNT162b2_2_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_postest.txt

  ## BNT162b2; 2; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_2_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_covidadmitted*.rds
      moderately_sensitive:
        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_update.R BNT162b2 2 covidadmitted
    needs:
    - preflight_BNT162b2_2_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_covidadmitted.txt

  ## BNT162b2; 2; covidemergency 
  ## preflight checks 

  preflight_BNT162b2_2_covidemergency:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_2_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 covidemergency
    needs:
    - preflight_BNT162b2_2_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_covidemergency.txt

  ## BNT162b2; 2; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_2_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_coviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 2 coviddeath
    needs:
    - preflight_BNT162b2_2_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_coviddeath.txt

  ## BNT162b2; 2; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_2_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 2 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_2_noncoviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 2 noncoviddeath
    needs:
    - preflight_BNT162b2_2_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_noncoviddeath.txt

  ## BNT162b2; 3; anytest 
  ## preflight checks 

  preflight_BNT162b2_3_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 anytest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_anytest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 3 anytest
    needs:
    - preflight_BNT162b2_3_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_anytest.txt

  ## BNT162b2; 3; postest 
  ## preflight checks 

  preflight_BNT162b2_3_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 postest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_postest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 3 postest
    needs:
    - preflight_BNT162b2_3_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_postest.txt

  ## BNT162b2; 3; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_3_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_covidadmitted*.rds
      moderately_sensitive:
        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_update.R BNT162b2 3 covidadmitted
    needs:
    - preflight_BNT162b2_3_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_covidadmitted.txt

  ## BNT162b2; 3; covidemergency 
  ## preflight checks 

  preflight_BNT162b2_3_covidemergency:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_3_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 covidemergency
    needs:
    - preflight_BNT162b2_3_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_covidemergency.txt

  ## BNT162b2; 3; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_3_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_coviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 3 coviddeath
    needs:
    - preflight_BNT162b2_3_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_coviddeath.txt

  ## BNT162b2; 3; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_3_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 3 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_3_noncoviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 3 noncoviddeath
    needs:
    - preflight_BNT162b2_3_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_noncoviddeath.txt

  ## BNT162b2; 4; anytest 
  ## preflight checks 

  preflight_BNT162b2_4_anytest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 anytest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_anytest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 4 anytest
    needs:
    - preflight_BNT162b2_4_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_anytest.txt

  ## BNT162b2; 4; postest 
  ## preflight checks 

  preflight_BNT162b2_4_postest:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 postest
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_postest*.rds
      moderately_sensitive:
        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_update.R BNT162b2 4 postest
    needs:
    - preflight_BNT162b2_4_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_postest.txt

  ## BNT162b2; 4; covidadmitted 
  ## preflight checks 

  preflight_BNT162b2_4_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_covidadmitted*.rds
      moderately_sensitive:
        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_update.R BNT162b2 4 covidadmitted
    needs:
    - preflight_BNT162b2_4_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_covidadmitted.txt

  ## BNT162b2; 4; covidemergency 
  ## preflight checks 

  preflight_BNT162b2_4_covidemergency:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_BNT162b2_4_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 covidemergency
    needs:
    - preflight_BNT162b2_4_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_covidemergency.txt

  ## BNT162b2; 4; coviddeath 
  ## preflight checks 

  preflight_BNT162b2_4_coviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_coviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 4 coviddeath
    needs:
    - preflight_BNT162b2_4_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_coviddeath.txt

  ## BNT162b2; 4; noncoviddeath 
  ## preflight checks 

  preflight_BNT162b2_4_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R BNT162b2 4 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_BNT162b2_4_noncoviddeath*.rds
      moderately_sensitive:
        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_update.R BNT162b2 4 noncoviddeath
    needs:
    - preflight_BNT162b2_4_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_noncoviddeath.txt

  ## ChAdOx1; 1; anytest 
  ## preflight checks 

  preflight_ChAdOx1_1_anytest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 anytest
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_1_anytest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_anytest*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_1_anytest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 anytest
    needs:
    - preflight_ChAdOx1_1_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_1_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_anytest.txt

  ## ChAdOx1; 1; postest 
  ## preflight checks 

  preflight_ChAdOx1_1_postest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 postest
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_1_postest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_postest*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_1_postest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 postest
    needs:
    - preflight_ChAdOx1_1_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_1_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_postest.txt

  ## ChAdOx1; 1; covidadmitted 
  ## preflight checks 

  preflight_ChAdOx1_1_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_1_covidadmitted*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_covidadmitted*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_1_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 covidadmitted
    needs:
    - preflight_ChAdOx1_1_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_1_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_covidadmitted.txt

  ## ChAdOx1; 1; covidemergency 
  ## preflight checks 

  preflight_ChAdOx1_1_covidemergency:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_1_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_1_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 covidemergency
    needs:
    - preflight_ChAdOx1_1_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_1_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_covidemergency.txt

  ## ChAdOx1; 1; coviddeath 
  ## preflight checks 

  preflight_ChAdOx1_1_coviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_1_coviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_coviddeath*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_1_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 coviddeath
    needs:
    - preflight_ChAdOx1_1_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_1_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_coviddeath.txt

  ## ChAdOx1; 1; noncoviddeath 
  ## preflight checks 

  preflight_ChAdOx1_1_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_1_noncoviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_noncoviddeath*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_1_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 noncoviddeath
    needs:
    - preflight_ChAdOx1_1_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_1_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_noncoviddeath.txt

  ## ChAdOx1; 2; anytest 
  ## preflight checks 

  preflight_ChAdOx1_2_anytest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 anytest
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_2_anytest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_anytest*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_2_anytest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 anytest
    needs:
    - preflight_ChAdOx1_2_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_2_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_anytest.txt

  ## ChAdOx1; 2; postest 
  ## preflight checks 

  preflight_ChAdOx1_2_postest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 postest
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_2_postest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_postest*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_2_postest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 postest
    needs:
    - preflight_ChAdOx1_2_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_2_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_postest.txt

  ## ChAdOx1; 2; covidadmitted 
  ## preflight checks 

  preflight_ChAdOx1_2_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_2_covidadmitted*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_covidadmitted*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_2_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 covidadmitted
    needs:
    - preflight_ChAdOx1_2_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_2_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_covidadmitted.txt

  ## ChAdOx1; 2; covidemergency 
  ## preflight checks 

  preflight_ChAdOx1_2_covidemergency:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_2_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_2_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 covidemergency
    needs:
    - preflight_ChAdOx1_2_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_2_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_covidemergency.txt

  ## ChAdOx1; 2; coviddeath 
  ## preflight checks 

  preflight_ChAdOx1_2_coviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_2_coviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_coviddeath*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_2_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 coviddeath
    needs:
    - preflight_ChAdOx1_2_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_2_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_coviddeath.txt

  ## ChAdOx1; 2; noncoviddeath 
  ## preflight checks 

  preflight_ChAdOx1_2_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_2_noncoviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_noncoviddeath*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_2_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 noncoviddeath
    needs:
    - preflight_ChAdOx1_2_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_2_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_noncoviddeath.txt

  ## ChAdOx1; 3; anytest 
  ## preflight checks 

  preflight_ChAdOx1_3_anytest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 anytest
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_3_anytest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_anytest*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_3_anytest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 anytest
    needs:
    - preflight_ChAdOx1_3_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_3_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_anytest.txt

  ## ChAdOx1; 3; postest 
  ## preflight checks 

  preflight_ChAdOx1_3_postest:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 postest
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_3_postest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_postest*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_3_postest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 postest
    needs:
    - preflight_ChAdOx1_3_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_3_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_postest.txt

  ## ChAdOx1; 3; covidadmitted 
  ## preflight checks 

  preflight_ChAdOx1_3_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_3_covidadmitted*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_covidadmitted*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_3_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 covidadmitted
    needs:
    - preflight_ChAdOx1_3_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_3_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_covidadmitted.txt

  ## ChAdOx1; 3; covidemergency 
  ## preflight checks 

  preflight_ChAdOx1_3_covidemergency:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_3_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_3_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 covidemergency
    needs:
    - preflight_ChAdOx1_3_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_3_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_covidemergency.txt

  ## ChAdOx1; 3; coviddeath 
  ## preflight checks 

  preflight_ChAdOx1_3_coviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_3_coviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_coviddeath*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_3_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 coviddeath
    needs:
    - preflight_ChAdOx1_3_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_3_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_coviddeath.txt

  ## ChAdOx1; 3; noncoviddeath 
  ## preflight checks 

  preflight_ChAdOx1_3_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_ChAdOx1
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_ChAdOx1_3_noncoviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_noncoviddeath*.txt

  ## apply cox model 

  apply_model_cox_ChAdOx1_3_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 noncoviddeath
    needs:
    - preflight_ChAdOx1_3_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx1_3_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_noncoviddeath.txt

  ## both; 1; anytest 
  ## preflight checks 

  preflight_both_1_anytest:
    run: r:latest analysis/comparisons/preflight.R both 1 anytest
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_anytest*.rds
      moderately_sensitive:
        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_update.R both 1 anytest
    needs:
    - preflight_both_1_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_1_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_anytest.txt

  ## both; 1; postest 
  ## preflight checks 

  preflight_both_1_postest:
    run: r:latest analysis/comparisons/preflight.R both 1 postest
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_postest*.rds
      moderately_sensitive:
        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_update.R both 1 postest
    needs:
    - preflight_both_1_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_1_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_postest.txt

  ## both; 1; covidadmitted 
  ## preflight checks 

  preflight_both_1_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R both 1 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_covidadmitted*.rds
      moderately_sensitive:
        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_update.R both 1 covidadmitted
    needs:
    - preflight_both_1_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_1_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_covidadmitted.txt

  ## both; 1; covidemergency 
  ## preflight checks 

  preflight_both_1_covidemergency:
    run: r:latest analysis/comparisons/preflight.R both 1 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_1_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_both_1_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 1 covidemergency
    needs:
    - preflight_both_1_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_1_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_covidemergency.txt

  ## both; 1; coviddeath 
  ## preflight checks 

  preflight_both_1_coviddeath:
    run: r:latest analysis/comparisons/preflight.R both 1 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_coviddeath*.rds
      moderately_sensitive:
        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_update.R both 1 coviddeath
    needs:
    - preflight_both_1_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_1_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_coviddeath.txt

  ## both; 1; noncoviddeath 
  ## preflight checks 

  preflight_both_1_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R both 1 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_1_noncoviddeath*.rds
      moderately_sensitive:
        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_update.R both 1 noncoviddeath
    needs:
    - preflight_both_1_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_1_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_noncoviddeath.txt

  ## both; 2; anytest 
  ## preflight checks 

  preflight_both_2_anytest:
    run: r:latest analysis/comparisons/preflight.R both 2 anytest
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_2_anytest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_2_anytest*.txt

  ## apply cox model 

  apply_model_cox_both_2_anytest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 anytest
    needs:
    - preflight_both_2_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_2_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_2_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_anytest.txt

  ## both; 2; postest 
  ## preflight checks 

  preflight_both_2_postest:
    run: r:latest analysis/comparisons/preflight.R both 2 postest
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_2_postest*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_2_postest*.txt

  ## apply cox model 

  apply_model_cox_both_2_postest:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 postest
    needs:
    - preflight_both_2_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_2_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_2_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_postest.txt

  ## both; 2; covidadmitted 
  ## preflight checks 

  preflight_both_2_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R both 2 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_2_covidadmitted*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_2_covidadmitted*.txt

  ## apply cox model 

  apply_model_cox_both_2_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 covidadmitted
    needs:
    - preflight_both_2_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_2_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_2_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_covidadmitted.txt

  ## both; 2; covidemergency 
  ## preflight checks 

  preflight_both_2_covidemergency:
    run: r:latest analysis/comparisons/preflight.R both 2 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_2_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_2_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_both_2_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 covidemergency
    needs:
    - preflight_both_2_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_2_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_2_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_covidemergency.txt

  ## both; 2; coviddeath 
  ## preflight checks 

  preflight_both_2_coviddeath:
    run: r:latest analysis/comparisons/preflight.R both 2 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_2_coviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_2_coviddeath*.txt

  ## apply cox model 

  apply_model_cox_both_2_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 coviddeath
    needs:
    - preflight_both_2_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_2_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_2_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_coviddeath.txt

  ## both; 2; noncoviddeath 
  ## preflight checks 

  preflight_both_2_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R both 2 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_2_noncoviddeath*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_2_noncoviddeath*.txt

  ## apply cox model 

  apply_model_cox_both_2_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 noncoviddeath
    needs:
    - preflight_both_2_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_2_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_2_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_noncoviddeath.txt

  ## both; 3; anytest 
  ## preflight checks 

  preflight_both_3_anytest:
    run: r:latest analysis/comparisons/preflight.R both 3 anytest
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_anytest*.rds
      moderately_sensitive:
        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_update.R both 3 anytest
    needs:
    - preflight_both_3_anytest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_anytest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_anytest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_3_anytest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_anytest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_anytest.txt

  ## both; 3; postest 
  ## preflight checks 

  preflight_both_3_postest:
    run: r:latest analysis/comparisons/preflight.R both 3 postest
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_postest*.rds
      moderately_sensitive:
        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_update.R both 3 postest
    needs:
    - preflight_both_3_postest
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_postest*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_postest*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_3_postest*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_postest.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_postest.txt

  ## both; 3; covidadmitted 
  ## preflight checks 

  preflight_both_3_covidadmitted:
    run: r:latest analysis/comparisons/preflight.R both 3 covidadmitted
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_covidadmitted*.rds
      moderately_sensitive:
        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_update.R both 3 covidadmitted
    needs:
    - preflight_both_3_covidadmitted
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_covidadmitted*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_covidadmitted*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_3_covidadmitted*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_covidadmitted.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_covidadmitted.txt

  ## both; 3; covidemergency 
  ## preflight checks 

  preflight_both_3_covidemergency:
    run: r:latest analysis/comparisons/preflight.R both 3 covidemergency
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_covidemergency*.rds
      moderately_sensitive:
        preflight_report: output/preflight/tables/preflight_report_both_3_covidemergency*.txt

  ## apply cox model 

  apply_model_cox_both_3_covidemergency:
    run: r:latest analysis/comparisons/apply_model_cox_update.R both 3 covidemergency
    needs:
    - preflight_both_3_covidemergency
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_covidemergency*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_covidemergency*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_3_covidemergency*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_covidemergency.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_covidemergency.txt

  ## both; 3; coviddeath 
  ## preflight checks 

  preflight_both_3_coviddeath:
    run: r:latest analysis/comparisons/preflight.R both 3 coviddeath
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_coviddeath*.rds
      moderately_sensitive:
        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_update.R both 3 coviddeath
    needs:
    - preflight_both_3_coviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_coviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_coviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_3_coviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_coviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_coviddeath.txt

  ## both; 3; noncoviddeath 
  ## preflight checks 

  preflight_both_3_noncoviddeath:
    run: r:latest analysis/comparisons/preflight.R both 3 noncoviddeath
    needs:
    - data_covariates_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        model_input: output/preflight/data/model_input_both_3_noncoviddeath*.rds
      moderately_sensitive:
        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_update.R both 3 noncoviddeath
    needs:
    - preflight_both_3_noncoviddeath
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_noncoviddeath*.rds
        model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_noncoviddeath*.rds
        model_glance_rds: output/models_cox/data/modelcox_glance_both_3_noncoviddeath*.rds
      moderately_sensitive:
        model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_noncoviddeath.txt
        model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_noncoviddeath.txt

  ## combine all estimates for release 

  combine_estimates:
    run: r:latest analysis/comparisons/combine_estimates.R
    needs:
    - data_tte_process_BNT162b2
    - data_tte_process_ChAdOx1
    - apply_model_cox_BNT162b2_1_anytest
    - apply_model_cox_BNT162b2_1_postest
    - apply_model_cox_BNT162b2_1_covidadmitted
    - apply_model_cox_BNT162b2_1_covidemergency
    - apply_model_cox_BNT162b2_1_coviddeath
    - apply_model_cox_BNT162b2_1_noncoviddeath
    - apply_model_cox_BNT162b2_2_anytest
    - apply_model_cox_BNT162b2_2_postest
    - apply_model_cox_BNT162b2_2_covidadmitted
    - apply_model_cox_BNT162b2_2_covidemergency
    - apply_model_cox_BNT162b2_2_coviddeath
    - apply_model_cox_BNT162b2_2_noncoviddeath
    - apply_model_cox_BNT162b2_3_anytest
    - apply_model_cox_BNT162b2_3_postest
    - apply_model_cox_BNT162b2_3_covidadmitted
    - apply_model_cox_BNT162b2_3_covidemergency
    - apply_model_cox_BNT162b2_3_coviddeath
    - apply_model_cox_BNT162b2_3_noncoviddeath
    - apply_model_cox_BNT162b2_4_anytest
    - apply_model_cox_BNT162b2_4_postest
    - apply_model_cox_BNT162b2_4_covidadmitted
    - apply_model_cox_BNT162b2_4_covidemergency
    - apply_model_cox_BNT162b2_4_coviddeath
    - apply_model_cox_BNT162b2_4_noncoviddeath
    - apply_model_cox_ChAdOx1_1_anytest
    - apply_model_cox_ChAdOx1_1_postest
    - apply_model_cox_ChAdOx1_1_covidadmitted
    - apply_model_cox_ChAdOx1_1_covidemergency
    - apply_model_cox_ChAdOx1_1_coviddeath
    - apply_model_cox_ChAdOx1_1_noncoviddeath
    - apply_model_cox_ChAdOx1_2_anytest
    - apply_model_cox_ChAdOx1_2_postest
    - apply_model_cox_ChAdOx1_2_covidadmitted
    - apply_model_cox_ChAdOx1_2_covidemergency
    - apply_model_cox_ChAdOx1_2_coviddeath
    - apply_model_cox_ChAdOx1_2_noncoviddeath
    - apply_model_cox_ChAdOx1_3_anytest
    - apply_model_cox_ChAdOx1_3_postest
    - apply_model_cox_ChAdOx1_3_covidadmitted
    - apply_model_cox_ChAdOx1_3_covidemergency
    - apply_model_cox_ChAdOx1_3_coviddeath
    - apply_model_cox_ChAdOx1_3_noncoviddeath
    - apply_model_cox_both_1_anytest
    - apply_model_cox_both_1_postest
    - apply_model_cox_both_1_covidadmitted
    - apply_model_cox_both_1_covidemergency
    - apply_model_cox_both_1_coviddeath
    - apply_model_cox_both_1_noncoviddeath
    - apply_model_cox_both_2_anytest
    - apply_model_cox_both_2_postest
    - apply_model_cox_both_2_covidadmitted
    - apply_model_cox_both_2_covidemergency
    - apply_model_cox_both_2_coviddeath
    - apply_model_cox_both_2_noncoviddeath
    - apply_model_cox_both_3_anytest
    - apply_model_cox_both_3_postest
    - apply_model_cox_both_3_covidadmitted
    - apply_model_cox_both_3_covidemergency
    - apply_model_cox_both_3_coviddeath
    - apply_model_cox_both_3_noncoviddeath
    outputs:
      moderately_sensitive:
        event_counts_all: output/release_objects/event_counts*.csv
        estimates_all: output/release_objects/estimates*.csv

  ## #################################### 
  ## plot to check estimates 
  ## #################################### 

  plot_check:
    run: r:latest analysis/comparisons/plot_cox_check.R
    needs:
    - combine_estimates
    outputs:
      moderately_sensitive:
        plot_check: output/models_cox/images/plot_check*.svg

  ## #################################### 
  ## plot to check coefs 
  ## #################################### 

  plot_check_coefs:
    run: r:latest analysis/comparisons/plot_coefs.R
    needs:
    - combine_estimates
    outputs:
      moderately_sensitive:
        plot_coefs: output/models_cox/images/coefs*.png