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Job request: 4881

Workspace:
covid-ve-change-over-time--combine-jcvi-groups-in-model
ID:
cgeadmsqsttrjedk

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

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

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Show project.yaml
version: '3.0'

expectations:

  population_size: 100000

actions:

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

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

  ## #################################### 
  ## 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_covs: output/data/data_covs.rds
        data_vax_dates: output/data/data_*_vax_dates.rds
        data_long_dates: output/data/data_long_*_dates.rds
        data_covid_any: output/data/data_covid_any.rds
      moderately_sensitive:
        data_properties: output/tables/data_processed_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/lib/second_vax_period_dates.rds
      moderately_sensitive:
        second_vax_period_dates_txt: output/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 and d 

  data_eligible_cd:
    run: r:latest analysis/second_vax_period/data_eligible_cd.R
    needs:
    - design
    - data_input_process
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      highly_sensitive:
        data_eligible_c: output/data/data_eligible_c.rds
        data_eligible_d: output/data/data_eligible_d.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_cd
    outputs:
      highly_sensitive:
        data_comparisons: output/data/data_comparisons_*.rds

  ## process outcomes data 

  data_outcomes_process:
    run: r:latest analysis/comparisons/data_outcomes_process.R
    needs:
    - design
    - data_input_process
    - data_comparisons_process
    outputs:
      highly_sensitive:
        data_outcomes: output/data/data_outcomes_*.rds

  ## process tte data 

  data_tte_process:
    run: r:latest analysis/comparisons/data_tte_process.R
    needs:
    - design
    - data_comparisons_process
    - data_outcomes_process
    outputs:
      highly_sensitive:
        data_tte_brand_outcome: output/data/data_tte_*.rds

  ## apply models 
  ## subgroup = 02, comparison = BNT162b2, outcome = postest 

  apply_model_cox_02_BNT162b2_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R 02 BNT162b2 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_02_BNT162b2_postest.rds
        model_summary_rds: output/models/modelcox_summary_02_BNT162b2_postest.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_02_BNT162b2_postest_all.txt
        incidence_table_strata: output/tables/incidence_02_BNT162b2_postest_strata.txt
        model_glance: output/models/modelcox_glance_02_BNT162b2_postest.csv

  ## subgroup = 02, comparison = BNT162b2, outcome = covidadmitted 

  apply_model_cox_02_BNT162b2_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R 02 BNT162b2 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_02_BNT162b2_covidadmitted.rds
        model_summary_rds: output/models/modelcox_summary_02_BNT162b2_covidadmitted.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_02_BNT162b2_covidadmitted_all.txt
        incidence_table_strata: output/tables/incidence_02_BNT162b2_covidadmitted_strata.txt
        model_glance: output/models/modelcox_glance_02_BNT162b2_covidadmitted.csv

  ## subgroup = 02, comparison = BNT162b2, outcome = coviddeath 

  apply_model_cox_02_BNT162b2_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R 02 BNT162b2 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_02_BNT162b2_coviddeath.rds
        model_summary_rds: output/models/modelcox_summary_02_BNT162b2_coviddeath.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_02_BNT162b2_coviddeath_all.txt
        incidence_table_strata: output/tables/incidence_02_BNT162b2_coviddeath_strata.txt
        model_glance: output/models/modelcox_glance_02_BNT162b2_coviddeath.csv

  ## subgroup = 02, comparison = BNT162b2, outcome = death 

  apply_model_cox_02_BNT162b2_death:
    run: r:latest analysis/comparisons/apply_model_cox.R 02 BNT162b2 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_02_BNT162b2_death.rds
        model_summary_rds: output/models/modelcox_summary_02_BNT162b2_death.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_02_BNT162b2_death_all.txt
        incidence_table_strata: output/tables/incidence_02_BNT162b2_death_strata.txt
        model_glance: output/models/modelcox_glance_02_BNT162b2_death.csv

  ## subgroup = 03-10, comparison = BNT162b2, outcome = postest 

  apply_model_cox_03-10_BNT162b2_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 BNT162b2 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_BNT162b2_postest.rds
        model_summary_rds: output/models/modelcox_summary_03-10_BNT162b2_postest.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_BNT162b2_postest_all.txt
        incidence_table_strata: output/tables/incidence_03-10_BNT162b2_postest_strata.txt
        model_glance: output/models/modelcox_glance_03-10_BNT162b2_postest.csv

  ## subgroup = 03-10, comparison = BNT162b2, outcome = covidadmitted 

  apply_model_cox_03-10_BNT162b2_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 BNT162b2 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_BNT162b2_covidadmitted.rds
        model_summary_rds: output/models/modelcox_summary_03-10_BNT162b2_covidadmitted.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_BNT162b2_covidadmitted_all.txt
        incidence_table_strata: output/tables/incidence_03-10_BNT162b2_covidadmitted_strata.txt
        model_glance: output/models/modelcox_glance_03-10_BNT162b2_covidadmitted.csv

  ## subgroup = 03-10, comparison = BNT162b2, outcome = coviddeath 

  apply_model_cox_03-10_BNT162b2_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 BNT162b2 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_BNT162b2_coviddeath.rds
        model_summary_rds: output/models/modelcox_summary_03-10_BNT162b2_coviddeath.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_BNT162b2_coviddeath_all.txt
        incidence_table_strata: output/tables/incidence_03-10_BNT162b2_coviddeath_strata.txt
        model_glance: output/models/modelcox_glance_03-10_BNT162b2_coviddeath.csv

  ## subgroup = 03-10, comparison = BNT162b2, outcome = death 

  apply_model_cox_03-10_BNT162b2_death:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 BNT162b2 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_BNT162b2_death.rds
        model_summary_rds: output/models/modelcox_summary_03-10_BNT162b2_death.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_BNT162b2_death_all.txt
        incidence_table_strata: output/tables/incidence_03-10_BNT162b2_death_strata.txt
        model_glance: output/models/modelcox_glance_03-10_BNT162b2_death.csv

  ## subgroup = 03-10, comparison = ChAdOx, outcome = postest 

  apply_model_cox_03-10_ChAdOx_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 ChAdOx postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_ChAdOx_postest.rds
        model_summary_rds: output/models/modelcox_summary_03-10_ChAdOx_postest.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_ChAdOx_postest_all.txt
        incidence_table_strata: output/tables/incidence_03-10_ChAdOx_postest_strata.txt
        model_glance: output/models/modelcox_glance_03-10_ChAdOx_postest.csv

  ## subgroup = 03-10, comparison = ChAdOx, outcome = covidadmitted 

  apply_model_cox_03-10_ChAdOx_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 ChAdOx covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_ChAdOx_covidadmitted.rds
        model_summary_rds: output/models/modelcox_summary_03-10_ChAdOx_covidadmitted.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_ChAdOx_covidadmitted_all.txt
        incidence_table_strata: output/tables/incidence_03-10_ChAdOx_covidadmitted_strata.txt
        model_glance: output/models/modelcox_glance_03-10_ChAdOx_covidadmitted.csv

  ## subgroup = 03-10, comparison = ChAdOx, outcome = coviddeath 

  apply_model_cox_03-10_ChAdOx_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 ChAdOx coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_ChAdOx_coviddeath.rds
        model_summary_rds: output/models/modelcox_summary_03-10_ChAdOx_coviddeath.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_ChAdOx_coviddeath_all.txt
        incidence_table_strata: output/tables/incidence_03-10_ChAdOx_coviddeath_strata.txt
        model_glance: output/models/modelcox_glance_03-10_ChAdOx_coviddeath.csv

  ## subgroup = 03-10, comparison = ChAdOx, outcome = death 

  apply_model_cox_03-10_ChAdOx_death:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 ChAdOx death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_ChAdOx_death.rds
        model_summary_rds: output/models/modelcox_summary_03-10_ChAdOx_death.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_ChAdOx_death_all.txt
        incidence_table_strata: output/tables/incidence_03-10_ChAdOx_death_strata.txt
        model_glance: output/models/modelcox_glance_03-10_ChAdOx_death.csv

  ## subgroup = 03-10, comparison = both, outcome = postest 

  apply_model_cox_03-10_both_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 both postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_both_postest.rds
        model_summary_rds: output/models/modelcox_summary_03-10_both_postest.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_both_postest_all.txt
        incidence_table_strata: output/tables/incidence_03-10_both_postest_strata.txt
        model_glance: output/models/modelcox_glance_03-10_both_postest.csv

  ## subgroup = 03-10, comparison = both, outcome = covidadmitted 

  apply_model_cox_03-10_both_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 both covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_both_covidadmitted.rds
        model_summary_rds: output/models/modelcox_summary_03-10_both_covidadmitted.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_both_covidadmitted_all.txt
        incidence_table_strata: output/tables/incidence_03-10_both_covidadmitted_strata.txt
        model_glance: output/models/modelcox_glance_03-10_both_covidadmitted.csv

  ## subgroup = 03-10, comparison = both, outcome = coviddeath 

  apply_model_cox_03-10_both_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 both coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_both_coviddeath.rds
        model_summary_rds: output/models/modelcox_summary_03-10_both_coviddeath.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_both_coviddeath_all.txt
        incidence_table_strata: output/tables/incidence_03-10_both_coviddeath_strata.txt
        model_glance: output/models/modelcox_glance_03-10_both_coviddeath.csv

  ## subgroup = 03-10, comparison = both, outcome = death 

  apply_model_cox_03-10_both_death:
    run: r:latest analysis/comparisons/apply_model_cox.R 03-10 both death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_03-10_both_death.rds
        model_summary_rds: output/models/modelcox_summary_03-10_both_death.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_03-10_both_death_all.txt
        incidence_table_strata: output/tables/incidence_03-10_both_death_strata.txt
        model_glance: output/models/modelcox_glance_03-10_both_death.csv

  ## subgroup = 11-12, comparison = BNT162b2, outcome = postest 

  apply_model_cox_11-12_BNT162b2_postest:
    run: r:latest analysis/comparisons/apply_model_cox.R 11-12 BNT162b2 postest
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_11-12_BNT162b2_postest.rds
        model_summary_rds: output/models/modelcox_summary_11-12_BNT162b2_postest.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_11-12_BNT162b2_postest_all.txt
        incidence_table_strata: output/tables/incidence_11-12_BNT162b2_postest_strata.txt
        model_glance: output/models/modelcox_glance_11-12_BNT162b2_postest.csv

  ## subgroup = 11-12, comparison = BNT162b2, outcome = covidadmitted 

  apply_model_cox_11-12_BNT162b2_covidadmitted:
    run: r:latest analysis/comparisons/apply_model_cox.R 11-12 BNT162b2 covidadmitted
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_11-12_BNT162b2_covidadmitted.rds
        model_summary_rds: output/models/modelcox_summary_11-12_BNT162b2_covidadmitted.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_11-12_BNT162b2_covidadmitted_all.txt
        incidence_table_strata: output/tables/incidence_11-12_BNT162b2_covidadmitted_strata.txt
        model_glance: output/models/modelcox_glance_11-12_BNT162b2_covidadmitted.csv

  ## subgroup = 11-12, comparison = BNT162b2, outcome = coviddeath 

  apply_model_cox_11-12_BNT162b2_coviddeath:
    run: r:latest analysis/comparisons/apply_model_cox.R 11-12 BNT162b2 coviddeath
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_11-12_BNT162b2_coviddeath.rds
        model_summary_rds: output/models/modelcox_summary_11-12_BNT162b2_coviddeath.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_11-12_BNT162b2_coviddeath_all.txt
        incidence_table_strata: output/tables/incidence_11-12_BNT162b2_coviddeath_strata.txt
        model_glance: output/models/modelcox_glance_11-12_BNT162b2_coviddeath.csv

  ## subgroup = 11-12, comparison = BNT162b2, outcome = death 

  apply_model_cox_11-12_BNT162b2_death:
    run: r:latest analysis/comparisons/apply_model_cox.R 11-12 BNT162b2 death
    needs:
    - design
    - data_comparisons_process
    - data_tte_process
    outputs:
      highly_sensitive:
        modelnumber: output/models/model*_11-12_BNT162b2_death.rds
        model_summary_rds: output/models/modelcox_summary_11-12_BNT162b2_death.rds
      moderately_sensitive:
        incidence_table_all: output/tables/incidence_11-12_BNT162b2_death_all.txt
        incidence_table_strata: output/tables/incidence_11-12_BNT162b2_death_strata.txt
        model_glance: output/models/modelcox_glance_11-12_BNT162b2_death.csv

  ## generate tables 
  ## tabulate cox model for all outcomes 

  tables_model_cox_02_BNT162b2:
    run: r:latest analysis/comparisons/tables_cox.R 02 BNT162b2
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process
    - apply_model_cox_02_BNT162b2_postest
    - apply_model_cox_02_BNT162b2_covidadmitted
    - apply_model_cox_02_BNT162b2_coviddeath
    - apply_model_cox_02_BNT162b2_death
    outputs:
      moderately_sensitive:
        table_glance: output/tables/modelcox_glance_02_BNT162b2.txt
        table_coefficients: output/tables/modelcox_coefficients_02_BNT162b2.txt

  ## tabulate cox model for all outcomes 

  tables_model_cox_03-10_BNT162b2:
    run: r:latest analysis/comparisons/tables_cox.R 03-10 BNT162b2
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process
    - apply_model_cox_03-10_BNT162b2_postest
    - apply_model_cox_03-10_BNT162b2_covidadmitted
    - apply_model_cox_03-10_BNT162b2_coviddeath
    - apply_model_cox_03-10_BNT162b2_death
    outputs:
      moderately_sensitive:
        table_glance: output/tables/modelcox_glance_03-10_BNT162b2.txt
        table_coefficients: output/tables/modelcox_coefficients_03-10_BNT162b2.txt

  ## tabulate cox model for all outcomes 

  tables_model_cox_03-10_ChAdOx:
    run: r:latest analysis/comparisons/tables_cox.R 03-10 ChAdOx
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process
    - apply_model_cox_03-10_ChAdOx_postest
    - apply_model_cox_03-10_ChAdOx_covidadmitted
    - apply_model_cox_03-10_ChAdOx_coviddeath
    - apply_model_cox_03-10_ChAdOx_death
    outputs:
      moderately_sensitive:
        table_glance: output/tables/modelcox_glance_03-10_ChAdOx.txt
        table_coefficients: output/tables/modelcox_coefficients_03-10_ChAdOx.txt

  ## tabulate cox model for all outcomes 

  tables_model_cox_03-10_both:
    run: r:latest analysis/comparisons/tables_cox.R 03-10 both
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process
    - apply_model_cox_03-10_both_postest
    - apply_model_cox_03-10_both_covidadmitted
    - apply_model_cox_03-10_both_coviddeath
    - apply_model_cox_03-10_both_death
    outputs:
      moderately_sensitive:
        table_glance: output/tables/modelcox_glance_03-10_both.txt
        table_coefficients: output/tables/modelcox_coefficients_03-10_both.txt

  ## tabulate cox model for all outcomes 

  tables_model_cox_11-12_BNT162b2:
    run: r:latest analysis/comparisons/tables_cox.R 11-12 BNT162b2
    needs:
    - design
    - data_2nd_vax_dates
    - data_tte_process
    - apply_model_cox_11-12_BNT162b2_postest
    - apply_model_cox_11-12_BNT162b2_covidadmitted
    - apply_model_cox_11-12_BNT162b2_coviddeath
    - apply_model_cox_11-12_BNT162b2_death
    outputs:
      moderately_sensitive:
        table_glance: output/tables/modelcox_glance_11-12_BNT162b2.txt
        table_coefficients: output/tables/modelcox_coefficients_11-12_BNT162b2.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_02_BNT162b2_postest
    - apply_model_cox_02_BNT162b2_covidadmitted
    - apply_model_cox_02_BNT162b2_coviddeath
    - apply_model_cox_02_BNT162b2_death
    - apply_model_cox_03-10_BNT162b2_postest
    - apply_model_cox_03-10_BNT162b2_covidadmitted
    - apply_model_cox_03-10_BNT162b2_coviddeath
    - apply_model_cox_03-10_BNT162b2_death
    - apply_model_cox_11-12_BNT162b2_postest
    - apply_model_cox_11-12_BNT162b2_covidadmitted
    - apply_model_cox_11-12_BNT162b2_coviddeath
    - apply_model_cox_11-12_BNT162b2_death
    outputs:
      moderately_sensitive:
        plot: output/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_03-10_ChAdOx_postest
    - apply_model_cox_03-10_ChAdOx_covidadmitted
    - apply_model_cox_03-10_ChAdOx_coviddeath
    - apply_model_cox_03-10_ChAdOx_death
    outputs:
      moderately_sensitive:
        plot: output/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_03-10_BNT162b2_postest
    - apply_model_cox_03-10_BNT162b2_covidadmitted
    - apply_model_cox_03-10_BNT162b2_coviddeath
    - apply_model_cox_03-10_BNT162b2_death
    - apply_model_cox_03-10_ChAdOx_postest
    - apply_model_cox_03-10_ChAdOx_covidadmitted
    - apply_model_cox_03-10_ChAdOx_coviddeath
    - apply_model_cox_03-10_ChAdOx_death
    outputs:
      moderately_sensitive:
        plot: output/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_03-10_both_postest
    - apply_model_cox_03-10_both_covidadmitted
    - apply_model_cox_03-10_both_coviddeath
    - apply_model_cox_03-10_both_death
    outputs:
      moderately_sensitive:
        plot: output/images/plot_res_BNT162b2vsChAdOx.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Elsie Horne
Branch
combine-jcvi-groups-in-model
Force run dependencies
No
Git commit hash
6076c3b
Requested actions
  • plot_model_cox_BNT162b2
  • plot_model_cox_ChAdOx
  • plot_model_cox_BNT162b2andChAdOx
  • plot_model_cox_BNT162b2vsChAdOx