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 Change in effectiveness of COVID-19 vaccination over time in fully vaccinated individuals 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.

Jobs

ID Status Action
mr3uuy2a3qp4lbu4 succeeded plot_model_cox_BNT162b2vsChAdOx

Pipeline

Show Hide 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
        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_all: output/data/data_*.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/lib/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:
    - 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

  ## #################################### 
  ## 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
    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
    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
    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
    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_BNT162b2:
    run: r:latest analysis/comparisons/process_event_count_tables.R BNT162b2
    needs:
    - design
    - data_tte_process_BNT162b2
    outputs:
      moderately_sensitive:
        tables_events: output/tte/tables/events_BNT162b2*.csv
        tidy_tables_events: output/tte/tables/tidy_events_BNT162b2*.txt

  process_event_count_tables_ChAdOx:
    run: r:latest analysis/comparisons/process_event_count_tables.R ChAdOx
    needs:
    - design
    - data_tte_process_ChAdOx
    outputs:
      moderately_sensitive:
        tables_events: output/tte/tables/events_ChAdOx*.csv
        tidy_tables_events: output/tte/tables/tidy_events_ChAdOx*.txt

  process_event_count_tables_both:
    run: r:latest analysis/comparisons/process_event_count_tables.R both
    needs:
    - design
    - data_tte_process_both
    outputs:
      moderately_sensitive:
        tables_events: output/tte/tables/events_both*.csv
        tidy_tables_events: output/tte/tables/tidy_events_both*.txt

  ## apply models 
  ## BNT162b2; 16-64 and clinically vulnerable; postest 

  apply_model_cox_BNT162b2_1_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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 and clinically vulnerable; covidadmitted 

  apply_model_cox_BNT162b2_1_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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 and clinically vulnerable; coviddeath 

  apply_model_cox_BNT162b2_1_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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 and clinically vulnerable; noncoviddeath 

  apply_model_cox_BNT162b2_1_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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

  ## BNT162b2; 16-64 and clinically vulnerable; death 

  apply_model_cox_BNT162b2_1_death:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 1 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_1_death.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_death.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_death.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_postest
    - apply_model_cox_BNT162b2_1_covidadmitted
    - apply_model_cox_BNT162b2_1_coviddeath
    - apply_model_cox_BNT162b2_1_noncoviddeath
    - apply_model_cox_BNT162b2_1_death
    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; postest 

  apply_model_cox_BNT162b2_2_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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; covidadmitted 

  apply_model_cox_BNT162b2_2_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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; coviddeath 

  apply_model_cox_BNT162b2_2_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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; noncoviddeath 

  apply_model_cox_BNT162b2_2_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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

  ## BNT162b2; 18-39; death 

  apply_model_cox_BNT162b2_2_death:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 2 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_2_death.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_death.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_death.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_postest
    - apply_model_cox_BNT162b2_2_covidadmitted
    - apply_model_cox_BNT162b2_2_coviddeath
    - apply_model_cox_BNT162b2_2_noncoviddeath
    - apply_model_cox_BNT162b2_2_death
    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; postest 

  apply_model_cox_BNT162b2_3_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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; covidadmitted 

  apply_model_cox_BNT162b2_3_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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; coviddeath 

  apply_model_cox_BNT162b2_3_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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; noncoviddeath 

  apply_model_cox_BNT162b2_3_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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

  ## BNT162b2; 40-64; death 

  apply_model_cox_BNT162b2_3_death:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 3 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_3_death.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_death.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_death.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_postest
    - apply_model_cox_BNT162b2_3_covidadmitted
    - apply_model_cox_BNT162b2_3_coviddeath
    - apply_model_cox_BNT162b2_3_noncoviddeath
    - apply_model_cox_BNT162b2_3_death
    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+; postest 

  apply_model_cox_BNT162b2_4_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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+; covidadmitted 

  apply_model_cox_BNT162b2_4_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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+; coviddeath 

  apply_model_cox_BNT162b2_4_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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+; noncoviddeath 

  apply_model_cox_BNT162b2_4_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    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

  ## BNT162b2; 65+; death 

  apply_model_cox_BNT162b2_4_death:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 4 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_4_death.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_death.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_death.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_postest
    - apply_model_cox_BNT162b2_4_covidadmitted
    - apply_model_cox_BNT162b2_4_coviddeath
    - apply_model_cox_BNT162b2_4_noncoviddeath
    - apply_model_cox_BNT162b2_4_death
    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

  ## BNT162b2; all; postest 

  apply_model_cox_BNT162b2_5_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 5 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_5_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_5_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_5_postest.rds

  ## BNT162b2; all; covidadmitted 

  apply_model_cox_BNT162b2_5_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 5 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_5_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_5_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_5_covidadmitted.rds

  ## BNT162b2; all; coviddeath 

  apply_model_cox_BNT162b2_5_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 5 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_5_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_5_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_5_coviddeath.rds

  ## BNT162b2; all; noncoviddeath 

  apply_model_cox_BNT162b2_5_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 5 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_5_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_5_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_5_noncoviddeath.rds

  ## BNT162b2; all; death 

  apply_model_cox_BNT162b2_5_death:
    run: r:latest analysis/comparisons/apply_model_cox.R BNT162b2 5 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_BNT162b2
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_BNT162b2_5_death.rds
        model_summary: output/models_cox/data/modelcox_summary_BNT162b2_5_death.rds
        model_glance: output/models_cox/data/modelcox_glance_BNT162b2_5_death.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_BNT162b2_5:
    run: r:latest analysis/comparisons/tables_cox.R BNT162b2 5
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_BNT162b2
    - apply_model_cox_BNT162b2_5_postest
    - apply_model_cox_BNT162b2_5_covidadmitted
    - apply_model_cox_BNT162b2_5_coviddeath
    - apply_model_cox_BNT162b2_5_noncoviddeath
    - apply_model_cox_BNT162b2_5_death
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_5.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_5.txt

  ## ChAdOx; 16-64 and clinically vulnerable; postest 

  apply_model_cox_ChAdOx_1_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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 and clinically vulnerable; covidadmitted 

  apply_model_cox_ChAdOx_1_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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 and clinically vulnerable; coviddeath 

  apply_model_cox_ChAdOx_1_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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 and clinically vulnerable; noncoviddeath 

  apply_model_cox_ChAdOx_1_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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

  ## ChAdOx; 16-64 and clinically vulnerable; death 

  apply_model_cox_ChAdOx_1_death:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_1_death.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_death.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_death.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_postest
    - apply_model_cox_ChAdOx_1_covidadmitted
    - apply_model_cox_ChAdOx_1_coviddeath
    - apply_model_cox_ChAdOx_1_noncoviddeath
    - apply_model_cox_ChAdOx_1_death
    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; postest 

  apply_model_cox_ChAdOx_3_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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; covidadmitted 

  apply_model_cox_ChAdOx_3_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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; coviddeath 

  apply_model_cox_ChAdOx_3_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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; noncoviddeath 

  apply_model_cox_ChAdOx_3_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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

  ## ChAdOx; 40-64; death 

  apply_model_cox_ChAdOx_3_death:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_3_death.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_death.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_death.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_postest
    - apply_model_cox_ChAdOx_3_covidadmitted
    - apply_model_cox_ChAdOx_3_coviddeath
    - apply_model_cox_ChAdOx_3_noncoviddeath
    - apply_model_cox_ChAdOx_3_death
    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+; postest 

  apply_model_cox_ChAdOx_4_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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+; covidadmitted 

  apply_model_cox_ChAdOx_4_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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+; coviddeath 

  apply_model_cox_ChAdOx_4_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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+; noncoviddeath 

  apply_model_cox_ChAdOx_4_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    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

  ## ChAdOx; 65+; death 

  apply_model_cox_ChAdOx_4_death:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_4_death.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_death.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_death.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_postest
    - apply_model_cox_ChAdOx_4_covidadmitted
    - apply_model_cox_ChAdOx_4_coviddeath
    - apply_model_cox_ChAdOx_4_noncoviddeath
    - apply_model_cox_ChAdOx_4_death
    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

  ## ChAdOx; all; postest 

  apply_model_cox_ChAdOx_5_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 5 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_5_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_5_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_5_postest.rds

  ## ChAdOx; all; covidadmitted 

  apply_model_cox_ChAdOx_5_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 5 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_5_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_5_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_5_covidadmitted.rds

  ## ChAdOx; all; coviddeath 

  apply_model_cox_ChAdOx_5_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 5 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_5_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_5_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_5_coviddeath.rds

  ## ChAdOx; all; noncoviddeath 

  apply_model_cox_ChAdOx_5_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 5 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_5_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_5_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_5_noncoviddeath.rds

  ## ChAdOx; all; death 

  apply_model_cox_ChAdOx_5_death:
    run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 5 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_ChAdOx
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_ChAdOx_5_death.rds
        model_summary: output/models_cox/data/modelcox_summary_ChAdOx_5_death.rds
        model_glance: output/models_cox/data/modelcox_glance_ChAdOx_5_death.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_ChAdOx_5:
    run: r:latest analysis/comparisons/tables_cox.R ChAdOx 5
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_ChAdOx
    - apply_model_cox_ChAdOx_5_postest
    - apply_model_cox_ChAdOx_5_covidadmitted
    - apply_model_cox_ChAdOx_5_coviddeath
    - apply_model_cox_ChAdOx_5_noncoviddeath
    - apply_model_cox_ChAdOx_5_death
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_ChAdOx_5.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_ChAdOx_5.txt

  ## both; 16-64 and clinically vulnerable; postest 

  apply_model_cox_both_1_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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 and clinically vulnerable; covidadmitted 

  apply_model_cox_both_1_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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 and clinically vulnerable; coviddeath 

  apply_model_cox_both_1_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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 and clinically vulnerable; noncoviddeath 

  apply_model_cox_both_1_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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

  ## both; 16-64 and clinically vulnerable; death 

  apply_model_cox_both_1_death:
    run: r:latest analysis/comparisons/apply_model_cox.R both 1 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_1_death.rds
        model_summary: output/models_cox/data/modelcox_summary_both_1_death.rds
        model_glance: output/models_cox/data/modelcox_glance_both_1_death.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_postest
    - apply_model_cox_both_1_covidadmitted
    - apply_model_cox_both_1_coviddeath
    - apply_model_cox_both_1_noncoviddeath
    - apply_model_cox_both_1_death
    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; postest 

  apply_model_cox_both_3_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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; covidadmitted 

  apply_model_cox_both_3_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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; coviddeath 

  apply_model_cox_both_3_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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; noncoviddeath 

  apply_model_cox_both_3_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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

  ## both; 40-64; death 

  apply_model_cox_both_3_death:
    run: r:latest analysis/comparisons/apply_model_cox.R both 3 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_3_death.rds
        model_summary: output/models_cox/data/modelcox_summary_both_3_death.rds
        model_glance: output/models_cox/data/modelcox_glance_both_3_death.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_postest
    - apply_model_cox_both_3_covidadmitted
    - apply_model_cox_both_3_coviddeath
    - apply_model_cox_both_3_noncoviddeath
    - apply_model_cox_both_3_death
    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+; postest 

  apply_model_cox_both_4_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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+; covidadmitted 

  apply_model_cox_both_4_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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+; coviddeath 

  apply_model_cox_both_4_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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+; noncoviddeath 

  apply_model_cox_both_4_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    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

  ## both; 65+; death 

  apply_model_cox_both_4_death:
    run: r:latest analysis/comparisons/apply_model_cox.R both 4 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_4_death.rds
        model_summary: output/models_cox/data/modelcox_summary_both_4_death.rds
        model_glance: output/models_cox/data/modelcox_glance_both_4_death.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_postest
    - apply_model_cox_both_4_covidadmitted
    - apply_model_cox_both_4_coviddeath
    - apply_model_cox_both_4_noncoviddeath
    - apply_model_cox_both_4_death
    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

  ## both; all; postest 

  apply_model_cox_both_5_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R both 5 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_5_postest.rds
        model_summary: output/models_cox/data/modelcox_summary_both_5_postest.rds
        model_glance: output/models_cox/data/modelcox_glance_both_5_postest.rds

  ## both; all; covidadmitted 

  apply_model_cox_both_5_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R both 5 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_5_covidadmitted.rds
        model_summary: output/models_cox/data/modelcox_summary_both_5_covidadmitted.rds
        model_glance: output/models_cox/data/modelcox_glance_both_5_covidadmitted.rds

  ## both; all; coviddeath 

  apply_model_cox_both_5_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 5 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_5_coviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_5_coviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_5_coviddeath.rds

  ## both; all; noncoviddeath 

  apply_model_cox_both_5_noncoviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R both 5 noncoviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_5_noncoviddeath.rds
        model_summary: output/models_cox/data/modelcox_summary_both_5_noncoviddeath.rds
        model_glance: output/models_cox/data/modelcox_glance_both_5_noncoviddeath.rds

  ## both; all; death 

  apply_model_cox_both_5_death:
    run: r:latest analysis/comparisons/apply_model_cox.R both 5 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process_both
    outputs:
      highly_sensitive:
        modelnumber: output/models_cox/data/model*_both_5_death.rds
        model_summary: output/models_cox/data/modelcox_summary_both_5_death.rds
        model_glance: output/models_cox/data/modelcox_glance_both_5_death.rds

  ## tabulate cox model for all outcomes 

  tables_model_cox_both_5:
    run: r:latest analysis/comparisons/tables_cox.R both 5
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process_both
    - apply_model_cox_both_5_postest
    - apply_model_cox_both_5_covidadmitted
    - apply_model_cox_both_5_coviddeath
    - apply_model_cox_both_5_noncoviddeath
    - apply_model_cox_both_5_death
    outputs:
      moderately_sensitive:
        table_glance: output/models_cox/tables/modelcox_glance_both_5.txt
        table_coefficients: output/models_cox/tables/modelcox_coefficients_both_5.txt

  ## generate plots 
  ## plot BNT162b2 

  plot_model_cox_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_1_death
    - apply_model_cox_BNT162b2_2_postest
    - apply_model_cox_BNT162b2_2_covidadmitted
    - apply_model_cox_BNT162b2_2_coviddeath
    - apply_model_cox_BNT162b2_2_noncoviddeath
    - apply_model_cox_BNT162b2_2_death
    - 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_3_death
    - 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_BNT162b2_4_death
    - apply_model_cox_BNT162b2_5_postest
    - apply_model_cox_BNT162b2_5_covidadmitted
    - apply_model_cox_BNT162b2_5_coviddeath
    - apply_model_cox_BNT162b2_5_noncoviddeath
    - apply_model_cox_BNT162b2_5_death
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/plot_res_BNT162b2_*.png

  ## plot ChAdOx 

  plot_model_cox_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_1_death
    - 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_3_death
    - apply_model_cox_ChAdOx_4_postest
    - apply_model_cox_ChAdOx_4_covidadmitted
    - apply_model_cox_ChAdOx_4_coviddeath
    - apply_model_cox_ChAdOx_4_noncoviddeath
    - apply_model_cox_ChAdOx_4_death
    - apply_model_cox_ChAdOx_5_postest
    - apply_model_cox_ChAdOx_5_covidadmitted
    - apply_model_cox_ChAdOx_5_coviddeath
    - apply_model_cox_ChAdOx_5_noncoviddeath
    - apply_model_cox_ChAdOx_5_death
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/plot_res_ChAdOx_*.png

  ## plot BNT162b2andChAdOx 

  plot_model_cox_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_1_death
    - 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_3_death
    - 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_BNT162b2_4_death
    - apply_model_cox_BNT162b2_5_postest
    - apply_model_cox_BNT162b2_5_covidadmitted
    - apply_model_cox_BNT162b2_5_coviddeath
    - apply_model_cox_BNT162b2_5_noncoviddeath
    - apply_model_cox_BNT162b2_5_death
    - 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_1_death
    - 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_3_death
    - apply_model_cox_ChAdOx_4_postest
    - apply_model_cox_ChAdOx_4_covidadmitted
    - apply_model_cox_ChAdOx_4_coviddeath
    - apply_model_cox_ChAdOx_4_noncoviddeath
    - apply_model_cox_ChAdOx_4_death
    - apply_model_cox_ChAdOx_5_postest
    - apply_model_cox_ChAdOx_5_covidadmitted
    - apply_model_cox_ChAdOx_5_coviddeath
    - apply_model_cox_ChAdOx_5_noncoviddeath
    - apply_model_cox_ChAdOx_5_death
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/plot_res_BNT162b2andChAdOx_*.png

  ## plot BNT162b2vsChAdOx 

  plot_model_cox_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_1_death
    - apply_model_cox_both_3_postest
    - apply_model_cox_both_3_covidadmitted
    - apply_model_cox_both_3_coviddeath
    - apply_model_cox_both_3_noncoviddeath
    - apply_model_cox_both_3_death
    - apply_model_cox_both_4_postest
    - apply_model_cox_both_4_covidadmitted
    - apply_model_cox_both_4_coviddeath
    - apply_model_cox_both_4_noncoviddeath
    - apply_model_cox_both_4_death
    - apply_model_cox_both_5_postest
    - apply_model_cox_both_5_covidadmitted
    - apply_model_cox_both_5_coviddeath
    - apply_model_cox_both_5_noncoviddeath
    - apply_model_cox_both_5_death
    outputs:
      moderately_sensitive:
        plot: output/models_cox/images/plot_res_BNT162b2vsChAdOx_*.png

State

State is inferred from the related Jobs.

Status: Succeeded

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  • Finished:
  • Runtime: 00:00:19

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