This page shows the technical details of what happened when authorised researcher Will Hulme requested one or more actions to be run against real patient data in the COVID-19 Vaccine Effectiveness 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
rcuzzoz3gsgr3bik succeeded design
twuiwduvck4mb545 succeeded models_over80s_postest_any_immuno
noyslzmi5nriprx7 failed report_ipw_over80s_postest_any_immuno
xy2ts7rs3lelelk3 succeeded report_over80s_postest_any_immuno

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 50000

actions:

  design:
    run: r:latest analysis/R/design.R
    outputs:
      moderately_sensitive:
        metadata: output/metadata/metadata*
        chars: output/metadata/baseline_characteristics.rds
        formula: output/metadata/list_formula.rds
        strata: output/metadata/list_strata.rds
        reweight: output/metadata/reweight_death.rds


##############################################################################
##############################################################################
  ## VE in over 80s (over80s)
##############################################################################
##############################################################################

  extract_over80s:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_over80s --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_over80s.csv.gz

  data_process_over80s:
    run: r:latest analysis/R/data_process.R over80s
    needs: [extract_over80s]
    outputs:
      highly_sensitive:
        data: output/over80s/data/data_processed.rds

  data_process_long_over80s:
    run: r:latest analysis/R/data_process_long.R over80s
    needs: [data_process_over80s]
    outputs:
      highly_sensitive:
        data1: output/over80s/data/data_long_vax_dates.rds
        data2: output/over80s/data/data_long_admission_dates.rds
        data3: output/over80s/data/data_long_admission_infectious_dates.rds
        data4: output/over80s/data/data_long_admission_noninfectious_dates.rds
        data5: output/over80s/data/data_long_pr_probable_covid_dates.rds
        data6: output/over80s/data/data_long_pr_suspected_covid_dates.rds
        data7: output/over80s/data/data_long_postest_dates.rds

  check_ethnicity_over80s:
    run: r:latest analysis/R/check_ethnicity.R over80s
    needs: [data_process_over80s]
    outputs:
      moderately_sensitive:
        tab: output/over80s/data/ethnicity_table*.txt

  data_properties_over80s:
    run: r:latest analysis/R/data_properties.R output/over80s/data/data_processed.rds output/over80s/data_properties
    needs: [data_process_over80s]
    outputs:
      moderately_sensitive:
        datasummary: output/over80s/data_properties/data_processed*.txt

  data_selection_over80s:
    run: r:latest analysis/R/data_selection.R over80s
    needs: [data_process_over80s]
    outputs:
      highly_sensitive:
        data: output/over80s/data/data_cohort.rds
      moderately_sensitive:
        flow: output/over80s/data/flowchart.csv

  descr_table1_over80s:
    run: r:latest analysis/R/descr_table1.R over80s
    needs: [design, data_selection_over80s]
    outputs:
      highly_sensitive:
        rds: output/over80s/descriptive/tables/*.rds
      moderately_sensitive:
        html: output/over80s/descriptive/tables/table1.html

  descr_irr_over80s:
    run: r:latest analysis/R/descr_tableirr.R over80s
    needs: [design, data_selection_over80s]
    outputs:
      moderately_sensitive:
        tables: output/over80s/descriptive/tables/table_irr.html
        csv: output/over80s/descriptive/tables/table_irr.csv

  data_stset_over80s:
    run: r:latest analysis/R/data_stset.R over80s 0.1
    needs: [design, data_selection_over80s, data_process_long_over80s]
    outputs:
      highly_sensitive:
        data1: output/over80s/data/data_fixed.rds
        data2: output/over80s/data/data_tte.rds
        data3: output/over80s/data/data_pt.rds

  data_samples_over80s:
    run: r:latest analysis/R/data_samples.R over80s 0.1
    needs: [design, data_stset_over80s]
    outputs:
      highly_sensitive:
        data: output/over80s/data/data_samples.rds

  descr_preflight_over80s:
    run: r:latest analysis/R/preflight.R over80s all 0.15
    needs: [design, data_stset_over80s]
    outputs:
      moderately_sensitive:
        html: output/over80s/descriptive/model-checks/*.html
        csv: output/over80s/descriptive/model-checks/*.csv

  descr_events_over80s:
    run: r:latest analysis/R/descr_events.R over80s
    needs: [design, data_stset_over80s]
    outputs:
      highly_sensitive:
        rds: output/over80s/descriptive/plots/*.rds
      moderately_sensitive:
        plots: output/over80s/descriptive/plots/*.svg
        tables: output/over80s/descriptive/tables/*.csv


  # data_properties_over80s_fixed:
  #   run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_fixed.rds output/over80s/data_properties
  #   needs: [data_stset_over80s]
  #   outputs:
  #     moderately_sensitive:
  #       datasummary: output/over80s/data_properties/data_wide_fixed*.txt
  #
  # data_properties_over80s_tte:
  #   run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_tte.rds output/over80s/data_properties
  #   needs: [data_stset_over80s]
  #   outputs:
  #     moderately_sensitive:
  #       datasummary: output/over80s/data_properties/data_wide_tte*.txt


#######################################
 ## OVERALL MODELS: positive test, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_over80s_postest_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s postest any all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/any/all/*/model*.rds
        data: output/over80s/postest/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/postest/any/all/*/weights*

  report_ipw_over80s_postest_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s postest any all
    needs: [design, models_over80s_postest_any_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/postest/any/all/*/broom*.rds
        gt: output/over80s/postest/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/postest/any/all/*/plot*.svg
        tables: output/over80s/postest/any/all/*/tab*.html
        data: output/over80s/postest/any/all/*/broom*.csv

  report_over80s_postest_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s postest any all
    needs: [design, models_over80s_postest_any_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/postest/any/all/*.svg
        tables: output/over80s/postest/any/all/*.csv

## pfizer vaccine

  models_over80s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s postest pfizer all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/pfizer/all/*/model*.rds
        data: output/over80s/postest/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/postest/pfizer/all/*/weights*

  report_ipw_over80s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s postest pfizer all
    needs: [design, models_over80s_postest_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/postest/pfizer/all/*/broom*.rds
        gt: output/over80s/postest/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/postest/pfizer/all/*/plot*.svg
        tables: output/over80s/postest/pfizer/all/*/tab*.html
        data: output/over80s/postest/pfizer/all/*/broom*.csv

  report_over80s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s postest pfizer all
    needs: [design, models_over80s_postest_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/postest/pfizer/all/*.svg
        tables: output/over80s/postest/pfizer/all/*.csv

## az vaccine

  models_over80s_postest_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s postest az all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/az/all/*/model*.rds
        data: output/over80s/postest/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/postest/az/all/*/weights*

  report_ipw_over80s_postest_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s postest az all
    needs: [design, models_over80s_postest_az_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/postest/az/all/*/broom*.rds
        gt: output/over80s/postest/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/postest/az/all/*/plot*.svg
        tables: output/over80s/postest/az/all/*/tab*.html
        data: output/over80s/postest/az/all/*/broom*.csv

  report_over80s_postest_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s postest az all
    needs: [design, models_over80s_postest_az_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/postest/az/all/*.svg
        tables: output/over80s/postest/az/all/*.csv


#######################################
 ## OVERALL MODELS: covid hospital admission, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_over80s_covidadmitted_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted any all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/covidadmitted/any/all/*/model*.rds
        data: output/over80s/covidadmitted/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/covidadmitted/any/all/*/weights*

  report_ipw_over80s_covidadmitted_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted any all
    needs: [design, models_over80s_covidadmitted_any_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/covidadmitted/any/all/*/broom*.rds
        gt: output/over80s/covidadmitted/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/covidadmitted/any/all/*/plot*.svg
        tables: output/over80s/covidadmitted/any/all/*/tab*.html
        data: output/over80s/covidadmitted/any/all/*/broom*.csv

  report_over80s_covidadmitted_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted any all
    needs: [design, models_over80s_covidadmitted_any_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/covidadmitted/any/all/*.svg
        tables: output/over80s/covidadmitted/any/all/*.csv


## pfizer vaccine

  models_over80s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted pfizer all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/covidadmitted/pfizer/all/*/model*.rds
        data: output/over80s/covidadmitted/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/covidadmitted/pfizer/all/*/weights*

  report_ipw_over80s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted pfizer all
    needs: [design, models_over80s_covidadmitted_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/covidadmitted/pfizer/all/*/broom*.rds
        gt: output/over80s/covidadmitted/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/covidadmitted/pfizer/all/*/plot*.svg
        tables: output/over80s/covidadmitted/pfizer/all/*/tab*.html
        data: output/over80s/covidadmitted/pfizer/all/*/broom*.csv

  report_over80s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted pfizer all
    needs: [design, models_over80s_covidadmitted_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/covidadmitted/pfizer/all/*.svg
        tables: output/over80s/covidadmitted/pfizer/all/*.csv

## az vaccine

  models_over80s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted az all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/covidadmitted/az/all/*/model*.rds
        data: output/over80s/covidadmitted/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/covidadmitted/az/all/*/weights*

  report_ipw_over80s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted az all
    needs: [design, models_over80s_covidadmitted_az_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/covidadmitted/az/all/*/broom*.rds
        gt: output/over80s/covidadmitted/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/covidadmitted/az/all/*/plot*.svg
        tables: output/over80s/covidadmitted/az/all/*/tab*.html
        data: output/over80s/covidadmitted/az/all/*/broom*.csv

  report_over80s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted az all
    needs: [design, models_over80s_covidadmitted_az_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/covidadmitted/az/all/*.svg
        tables: output/over80s/covidadmitted/az/all/*.csv



#######################################
 ## OVERALL MODELS: non-covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_over80s_noncoviddeath_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath any all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/noncoviddeath/any/all/*/model*.rds
        data: output/over80s/noncoviddeath/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/noncoviddeath/any/all/*/weights*

  report_ipw_over80s_noncoviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath any all
    needs: [design, models_over80s_noncoviddeath_any_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/noncoviddeath/any/all/*/broom*.rds
        gt: output/over80s/noncoviddeath/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/noncoviddeath/any/all/*/plot*.svg
        tables: output/over80s/noncoviddeath/any/all/*/tab*.html
        data: output/over80s/noncoviddeath/any/all/*/broom*.csv


  report_over80s_noncoviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath any all
    needs: [design, models_over80s_noncoviddeath_any_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/noncoviddeath/any/all/*.svg
        tables: output/over80s/noncoviddeath/any/all/*.csv


## pfizer vaccine

  models_over80s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath pfizer all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/noncoviddeath/pfizer/all/*/model*.rds
        data: output/over80s/noncoviddeath/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/noncoviddeath/pfizer/all/*/weights*

  report_ipw_over80s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath pfizer all
    needs: [design, models_over80s_noncoviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/noncoviddeath/pfizer/all/*/broom*.rds
        gt: output/over80s/noncoviddeath/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/noncoviddeath/pfizer/all/*/plot*.svg
        tables: output/over80s/noncoviddeath/pfizer/all/*/tab*.html
        data: output/over80s/noncoviddeath/pfizer/all/*/broom*.csv

  report_over80s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath pfizer all
    needs: [design, models_over80s_noncoviddeath_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/noncoviddeath/pfizer/all/*.svg
        tables: output/over80s/noncoviddeath/pfizer/all/*.csv

## az vaccine

  models_over80s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath az all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/noncoviddeath/az/all/*/model*.rds
        data: output/over80s/noncoviddeath/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/noncoviddeath/az/all/*/weights*

  report_ipw_over80s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath az all
    needs: [design, models_over80s_noncoviddeath_az_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/noncoviddeath/az/all/*/broom*.rds
        gt: output/over80s/noncoviddeath/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/noncoviddeath/az/all/*/plot*.svg
        tables: output/over80s/noncoviddeath/az/all/*/tab*.html
        data: output/over80s/noncoviddeath/az/all/*/broom*.csv

  report_over80s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath az all
    needs: [design, models_over80s_noncoviddeath_az_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/noncoviddeath/az/all/*.svg
        tables: output/over80s/noncoviddeath/az/all/*.csv




#######################################
 ## OVERALL MODELS: covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_over80s_coviddeath_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath any all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/coviddeath/any/all/*/model*.rds
        data: output/over80s/coviddeath/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/coviddeath/any/all/*/weights*

  report_ipw_over80s_coviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath any all
    needs: [design, models_over80s_coviddeath_any_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/coviddeath/any/all/*/broom*.rds
        gt: output/over80s/coviddeath/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/coviddeath/any/all/*/plot*.svg
        tables: output/over80s/coviddeath/any/all/*/tab*.html
        data: output/over80s/coviddeath/any/all/*/broom*.csv

  report_over80s_coviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath any all
    needs: [design, models_over80s_coviddeath_any_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/coviddeath/any/all/*.svg
        tables: output/over80s/coviddeath/any/all/*.csv


## pfizer vaccine

  models_over80s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath pfizer all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/coviddeath/pfizer/all/*/model*.rds
        data: output/over80s/coviddeath/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/coviddeath/pfizer/all/*/weights*

  report_ipw_over80s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath pfizer all
    needs: [design, models_over80s_coviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/coviddeath/pfizer/all/*/broom*.rds
        gt: output/over80s/coviddeath/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/coviddeath/pfizer/all/*/plot*.svg
        tables: output/over80s/coviddeath/pfizer/all/*/tab*.html
        data: output/over80s/coviddeath/pfizer/all/*/broom*.csv

  report_over80s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath pfizer all
    needs: [design, models_over80s_coviddeath_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/coviddeath/pfizer/all/*.svg
        tables: output/over80s/coviddeath/pfizer/all/*.csv

## az vaccine

  models_over80s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath az all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/coviddeath/az/all/*/model*.rds
        data: output/over80s/coviddeath/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/coviddeath/az/all/*/weights*

  report_ipw_over80s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath az all
    needs: [design, models_over80s_coviddeath_az_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/coviddeath/az/all/*/broom*.rds
        gt: output/over80s/coviddeath/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/coviddeath/az/all/*/plot*.svg
        tables: output/over80s/coviddeath/az/all/*/tab*.html
        data: output/over80s/coviddeath/az/all/*/broom*.csv

  report_over80s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath az all
    needs: [design, models_over80s_coviddeath_az_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/coviddeath/az/all/*.svg
        tables: output/over80s/coviddeath/az/all/*.csv



#######################################
 ## OVERALL MODELS: all-cause death, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_over80s_death_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s death any all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/death/any/all/*/model*.rds
        data: output/over80s/death/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/death/any/all/*/weights*

  report_ipw_over80s_death_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s death any all
    needs: [design, models_over80s_death_any_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/death/any/all/*/broom*.rds
        gt: output/over80s/death/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/death/any/all/*/plot*.svg
        tables: output/over80s/death/any/all/*/tab*.html
        data: output/over80s/death/any/all/*/broom*.csv

  report_over80s_death_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s death any all
    needs: [design, models_over80s_death_any_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/death/any/all/*.svg
        tables: output/over80s/death/any/all/*.csv

## pfizer vaccine

  models_over80s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s death pfizer all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/death/pfizer/all/*/model*.rds
        data: output/over80s/death/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/death/pfizer/all/*/weights*

  report_ipw_over80s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s death pfizer all
    needs: [design, models_over80s_death_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/death/pfizer/all/*/broom*.rds
        gt: output/over80s/death/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/death/pfizer/all/*/plot*.svg
        tables: output/over80s/death/pfizer/all/*/tab*.html
        data: output/over80s/death/pfizer/all/*/broom*.csv

  report_over80s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s death pfizer all
    needs: [design, models_over80s_death_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/death/pfizer/all/*.svg
        tables: output/over80s/death/pfizer/all/*.csv

## az vaccine

  models_over80s_death_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s death az all
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/death/az/all/*/model*.rds
        data: output/over80s/death/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/death/az/all/*/weights*

  report_ipw_over80s_death_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s death az all
    needs: [design, models_over80s_death_az_all]
    outputs:
      highly_sensitive:
        broom: output/over80s/death/az/all/*/broom*.rds
        gt: output/over80s/death/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/death/az/all/*/plot*.svg
        tables: output/over80s/death/az/all/*/tab*.html
        data: output/over80s/death/az/all/*/broom*.csv

  report_over80s_death_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s death az all
    needs: [design, models_over80s_death_az_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/death/az/all/*.svg
        tables: output/over80s/death/az/all/*.csv




#######################################
 ## IMMUNOSUPPRESSION MODELS: positive test, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_over80s_postest_any_immuno:
    run: r:latest analysis/R/dose_1/model_msm.R over80s postest any any_immunosuppression
    needs: [design, data_stset_over80s, data_samples_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/postest/any/any_immunosuppression/*/model*.rds
        data: output/over80s/postest/any/any_immunosuppression/*/data*.rds
      moderately_sensitive:
        weights: output/over80s/postest/any/any_immunosuppression/*/weights*

  report_ipw_over80s_postest_any_immuno:
    run: r:latest analysis/R/dose_1/report_ipw.R over80s postest any any_immunosuppression
    needs: [design, models_over80s_postest_any_immuno]
    outputs:
      highly_sensitive:
        broom: output/over80s/postest/any/any_immunosuppression/*/broom*.rds
        gt: output/over80s/postest/any/any_immunosuppression/*/gt*.rds
      moderately_sensitive:
        plots: output/over80s/postest/any/any_immunosuppression/*/plot*.svg
        tables: output/over80s/postest/any/any_immunosuppression/*/tab*.html
        data: output/over80s/postest/any/any_immunosuppression/*/broom*.csv

  report_over80s_postest_any_immuno:
    run: r:latest analysis/R/dose_1/report_msm.R over80s postest any any_immunosuppression
    needs: [design, models_over80s_postest_any_immuno]
    outputs:
      moderately_sensitive:
        plots: output/over80s/postest/any/any_immunosuppression/*.svg
        tables: output/over80s/postest/any/any_immunosuppression/*.csv



#######################################
 ## COMBINE OVERALL MODELS:
#######################################

  # report_over80s_any_all:
  #   run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s any all
  #   needs: [design, report_over80s_postest_any_all, report_over80s_covidadmitted_any_all, report_over80s_coviddeath_any_all, report_over80s_noncoviddeath_any_all, report_over80s_death_any_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/*any_all.svg
  #       tables: output/over80s/*any_all.csv
  #       html: output/over80s/*any_all.html
  #
  # report_over80s_pfizer_all:
  #   run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s pfizer all
  #   needs: [design, report_over80s_postest_pfizer_all, report_over80s_covidadmitted_pfizer_all, report_over80s_coviddeath_pfizer_all, report_over80s_noncoviddeath_pfizer_all, report_over80s_death_pfizer_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/*pfizer_all.svg
  #       tables: output/over80s/*pfizer_all.csv
  #       html: output/over80s/*pfizer_all.html
  #
  # report_over80s_az_all:
  #   run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s az all
  #   needs: [design, report_over80s_postest_az_all, report_over80s_covidadmitted_az_all, report_over80s_coviddeath_az_all, report_over80s_noncoviddeath_az_all, report_over80s_death_az_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/*az_all.svg
  #       tables: output/over80s/*az_all.csv
  #       html: output/over80s/*az_all.html


  report_ipw_over80s_all:
    run: r:latest analysis/R/dose_1/report_vaxmodel.R over80s death all
    needs: [design, report_ipw_over80s_death_any_all, report_ipw_over80s_death_pfizer_all, report_ipw_over80s_death_az_all]
    outputs:
      moderately_sensitive:
        svg: output/over80s/plot_vax1.svg
        #html: output/over80s/tab_vax1.html
        csv: output/over80s/tab_vax1.csv
        csv1: output/over80s/tab_vax1_wide.csv


  report_over80s_all:
    run: r:latest analysis/R/dose_1/report_alloutcomes_combined.R over80s all
    needs: [design, report_over80s_postest_any_all, report_over80s_covidadmitted_any_all, report_over80s_coviddeath_any_all, report_over80s_noncoviddeath_any_all, report_over80s_death_any_all,
    report_over80s_postest_pfizer_all, report_over80s_covidadmitted_pfizer_all, report_over80s_coviddeath_pfizer_all, report_over80s_noncoviddeath_pfizer_all, report_over80s_death_pfizer_all,
    report_over80s_postest_az_all, report_over80s_covidadmitted_az_all, report_over80s_coviddeath_az_all, report_over80s_noncoviddeath_az_all, report_over80s_death_az_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/*_all.svg
        plots1: output/over80s/*_all.png
        tables: output/over80s/*_all.csv






##############################################################################
##############################################################################
  ## VE in 70-79s
##############################################################################
##############################################################################

  extract_in70s:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_in70s --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_in70s.csv.gz

  data_process_in70s:
    run: r:latest analysis/R/data_process.R in70s
    needs: [extract_in70s]
    outputs:
      highly_sensitive:
        data: output/in70s/data/data_processed.rds

  data_process_long_in70s:
    run: r:latest analysis/R/data_process_long.R in70s
    needs: [data_process_in70s]
    outputs:
      highly_sensitive:
        data1: output/in70s/data/data_long_vax_dates.rds
        data2: output/in70s/data/data_long_admission_dates.rds
        data3: output/in70s/data/data_long_admission_infectious_dates.rds
        data4: output/in70s/data/data_long_admission_noninfectious_dates.rds
        data5: output/in70s/data/data_long_pr_probable_covid_dates.rds
        data6: output/in70s/data/data_long_pr_suspected_covid_dates.rds
        data7: output/in70s/data/data_long_postest_dates.rds

  check_ethnicity_in70s:
    run: r:latest analysis/R/check_ethnicity.R in70s
    needs: [data_process_in70s]
    outputs:
      moderately_sensitive:
        tab: output/in70s/data/ethnicity_table*.txt

  data_properties_in70s:
    run: r:latest analysis/R/data_properties.R output/in70s/data/data_processed.rds output/in70s/data_properties
    needs: [data_process_in70s]
    outputs:
      moderately_sensitive:
        datasummary: output/in70s/data_properties/data_processed*.txt

  data_selection_in70s:
    run: r:latest analysis/R/data_selection.R in70s
    needs: [data_process_in70s]
    outputs:
      highly_sensitive:
        data: output/in70s/data/data_cohort.rds
      moderately_sensitive:
        flow: output/in70s/data/flowchart.csv

  descr_table1_in70s:
    run: r:latest analysis/R/descr_table1.R in70s
    needs: [design, data_selection_in70s]
    outputs:
      highly_sensitive:
        rds: output/in70s/descriptive/tables/*.rds
      moderately_sensitive:
        html: output/in70s/descriptive/tables/table1.html

  descr_irr_in70s:
    run: r:latest analysis/R/descr_tableirr.R in70s
    needs: [design, data_selection_in70s]
    outputs:
      moderately_sensitive:
        tables: output/in70s/descriptive/tables/table_irr.html
        csv: output/in70s/descriptive/tables/table_irr.csv

  data_stset_in70s:
    run: r:latest analysis/R/data_stset.R in70s 0.05
    needs: [design, data_selection_in70s, data_process_long_in70s]
    outputs:
      highly_sensitive:
        data1: output/in70s/data/data_fixed.rds
        data2: output/in70s/data/data_tte.rds
        data3: output/in70s/data/data_pt.rds

  data_samples_in70s:
    run: r:latest analysis/R/data_samples.R in70s 0.05
    needs: [design, data_stset_in70s]
    outputs:
      highly_sensitive:
        data: output/in70s/data/data_samples.rds

  descr_preflight_in70s:
    run: r:latest analysis/R/preflight.R in70s all 0.05
    needs: [design, data_stset_in70s]
    outputs:
      moderately_sensitive:
        html: output/in70s/descriptive/model-checks/*.html
        csv: output/in70s/descriptive/model-checks/*.csv

  descr_events_in70s:
    run: r:latest analysis/R/descr_events.R in70s
    needs: [design, data_stset_in70s]
    outputs:
      highly_sensitive:
        rds: output/in70s/descriptive/plots/*.rds
      moderately_sensitive:
        plots: output/in70s/descriptive/plots/*.svg
        tables: output/in70s/descriptive/tables/*.csv


  # data_properties_in70s_fixed:
  #   run: r:latest analysis/R/data_properties.R output/in70s/data/data_wide_fixed.rds output/in70s/data_properties
  #   needs: [data_stset_in70s]
  #   outputs:
  #     moderately_sensitive:
  #       datasummary: output/in70s/data_properties/data_wide_fixed*.txt
  #
  # data_properties_in70s_tte:
  #   run: r:latest analysis/R/data_properties.R output/in70s/data/data_wide_tte.rds output/in70s/data_properties
  #   needs: [data_stset_in70s]
  #   outputs:
  #     moderately_sensitive:
  #       datasummary: output/in70s/data_properties/data_wide_tte*.txt


#######################################
 ## OVERALL MODELS: positive test, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_in70s_postest_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s postest any all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/postest/any/all/*/model*.rds
        data: output/in70s/postest/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/postest/any/all/*/weights*

  report_ipw_in70s_postest_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s postest any all
    needs: [design, models_in70s_postest_any_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/postest/any/all/*/broom*.rds
        gt: output/in70s/postest/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/postest/any/all/*/plot*.svg
        tables: output/in70s/postest/any/all/*/tab*.html
        data: output/in70s/postest/any/all/*/broom*.csv

  report_in70s_postest_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s postest any all
    needs: [design, models_in70s_postest_any_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/postest/any/all/*.svg
        tables: output/in70s/postest/any/all/*.csv

## pfizer vaccine

  models_in70s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s postest pfizer all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/postest/pfizer/all/*/model*.rds
        data: output/in70s/postest/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/postest/pfizer/all/*/weights*

  report_ipw_in70s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s postest pfizer all
    needs: [design, models_in70s_postest_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/postest/pfizer/all/*/broom*.rds
        gt: output/in70s/postest/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/postest/pfizer/all/*/plot*.svg
        tables: output/in70s/postest/pfizer/all/*/tab*.html
        data: output/in70s/postest/pfizer/all/*/broom*.csv

  report_in70s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s postest pfizer all
    needs: [design, models_in70s_postest_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/postest/pfizer/all/*.svg
        tables: output/in70s/postest/pfizer/all/*.csv

## az vaccine

  models_in70s_postest_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s postest az all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/postest/az/all/*/model*.rds
        data: output/in70s/postest/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/postest/az/all/*/weights*

  report_ipw_in70s_postest_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s postest az all
    needs: [design, models_in70s_postest_az_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/postest/az/all/*/broom*.rds
        gt: output/in70s/postest/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/postest/az/all/*/plot*.svg
        tables: output/in70s/postest/az/all/*/tab*.html
        data: output/in70s/postest/az/all/*/broom*.csv

  report_in70s_postest_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s postest az all
    needs: [design, models_in70s_postest_az_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/postest/az/all/*.svg
        tables: output/in70s/postest/az/all/*.csv


#######################################
 ## OVERALL MODELS: covid hospital admission, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_in70s_covidadmitted_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted any all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/covidadmitted/any/all/*/model*.rds
        data: output/in70s/covidadmitted/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/covidadmitted/any/all/*/weights*

  report_ipw_in70s_covidadmitted_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s covidadmitted any all
    needs: [design, models_in70s_covidadmitted_any_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/covidadmitted/any/all/*/broom*.rds
        gt: output/in70s/covidadmitted/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/covidadmitted/any/all/*/plot*.svg
        tables: output/in70s/covidadmitted/any/all/*/tab*.html
        data: output/in70s/covidadmitted/any/all/*/broom*.csv

  report_in70s_covidadmitted_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted any all
    needs: [design, models_in70s_covidadmitted_any_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/covidadmitted/any/all/*.svg
        tables: output/in70s/covidadmitted/any/all/*.csv


## pfizer vaccine

  models_in70s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted pfizer all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/covidadmitted/pfizer/all/*/model*.rds
        data: output/in70s/covidadmitted/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/covidadmitted/pfizer/all/*/weights*

  report_ipw_in70s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s covidadmitted pfizer all
    needs: [design, models_in70s_covidadmitted_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/covidadmitted/pfizer/all/*/broom*.rds
        gt: output/in70s/covidadmitted/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/covidadmitted/pfizer/all/*/plot*.svg
        tables: output/in70s/covidadmitted/pfizer/all/*/tab*.html
        data: output/in70s/covidadmitted/pfizer/all/*/broom*.csv

  report_in70s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted pfizer all
    needs: [design, models_in70s_covidadmitted_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/covidadmitted/pfizer/all/*.svg
        tables: output/in70s/covidadmitted/pfizer/all/*.csv

## az vaccine

  models_in70s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted az all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/covidadmitted/az/all/*/model*.rds
        data: output/in70s/covidadmitted/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/covidadmitted/az/all/*/weights*

  report_ipw_in70s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s covidadmitted az all
    needs: [design, models_in70s_covidadmitted_az_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/covidadmitted/az/all/*/broom*.rds
        gt: output/in70s/covidadmitted/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/covidadmitted/az/all/*/plot*.svg
        tables: output/in70s/covidadmitted/az/all/*/tab*.html
        data: output/in70s/covidadmitted/az/all/*/broom*.csv

  report_in70s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted az all
    needs: [design, models_in70s_covidadmitted_az_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/covidadmitted/az/all/*.svg
        tables: output/in70s/covidadmitted/az/all/*.csv



#######################################
 ## OVERALL MODELS: non-covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_in70s_noncoviddeath_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s noncoviddeath any all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/noncoviddeath/any/all/*/model*.rds
        data: output/in70s/noncoviddeath/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/noncoviddeath/any/all/*/weights*

  report_ipw_in70s_noncoviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s noncoviddeath any all
    needs: [design, models_in70s_noncoviddeath_any_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/noncoviddeath/any/all/*/broom*.rds
        gt: output/in70s/noncoviddeath/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/noncoviddeath/any/all/*/plot*.svg
        tables: output/in70s/noncoviddeath/any/all/*/tab*.html
        data: output/in70s/noncoviddeath/any/all/*/broom*.csv


  report_in70s_noncoviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath any all
    needs: [design, models_in70s_noncoviddeath_any_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/noncoviddeath/any/all/*.svg
        tables: output/in70s/noncoviddeath/any/all/*.csv


## pfizer vaccine

  models_in70s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s noncoviddeath pfizer all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/noncoviddeath/pfizer/all/*/model*.rds
        data: output/in70s/noncoviddeath/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/noncoviddeath/pfizer/all/*/weights*

  report_ipw_in70s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s noncoviddeath pfizer all
    needs: [design, models_in70s_noncoviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/noncoviddeath/pfizer/all/*/broom*.rds
        gt: output/in70s/noncoviddeath/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/noncoviddeath/pfizer/all/*/plot*.svg
        tables: output/in70s/noncoviddeath/pfizer/all/*/tab*.html
        data: output/in70s/noncoviddeath/pfizer/all/*/broom*.csv

  report_in70s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath pfizer all
    needs: [design, models_in70s_noncoviddeath_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/noncoviddeath/pfizer/all/*.svg
        tables: output/in70s/noncoviddeath/pfizer/all/*.csv

## az vaccine

  models_in70s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s noncoviddeath az all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/noncoviddeath/az/all/*/model*.rds
        data: output/in70s/noncoviddeath/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/noncoviddeath/az/all/*/weights*

  report_ipw_in70s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s noncoviddeath az all
    needs: [design, models_in70s_noncoviddeath_az_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/noncoviddeath/az/all/*/broom*.rds
        gt: output/in70s/noncoviddeath/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/noncoviddeath/az/all/*/plot*.svg
        tables: output/in70s/noncoviddeath/az/all/*/tab*.html
        data: output/in70s/noncoviddeath/az/all/*/broom*.csv

  report_in70s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath az all
    needs: [design, models_in70s_noncoviddeath_az_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/noncoviddeath/az/all/*.svg
        tables: output/in70s/noncoviddeath/az/all/*.csv




#######################################
 ## OVERALL MODELS: covid death, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_in70s_coviddeath_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s coviddeath any all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/coviddeath/any/all/*/model*.rds
        data: output/in70s/coviddeath/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/coviddeath/any/all/*/weights*

  report_ipw_in70s_coviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s coviddeath any all
    needs: [design, models_in70s_coviddeath_any_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/coviddeath/any/all/*/broom*.rds
        gt: output/in70s/coviddeath/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/coviddeath/any/all/*/plot*.svg
        tables: output/in70s/coviddeath/any/all/*/tab*.html
        data: output/in70s/coviddeath/any/all/*/broom*.csv

  report_in70s_coviddeath_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath any all
    needs: [design, models_in70s_coviddeath_any_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/coviddeath/any/all/*.svg
        tables: output/in70s/coviddeath/any/all/*.csv


## pfizer vaccine

  models_in70s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s coviddeath pfizer all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/coviddeath/pfizer/all/*/model*.rds
        data: output/in70s/coviddeath/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/coviddeath/pfizer/all/*/weights*

  report_ipw_in70s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s coviddeath pfizer all
    needs: [design, models_in70s_coviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/coviddeath/pfizer/all/*/broom*.rds
        gt: output/in70s/coviddeath/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/coviddeath/pfizer/all/*/plot*.svg
        tables: output/in70s/coviddeath/pfizer/all/*/tab*.html
        data: output/in70s/coviddeath/pfizer/all/*/broom*.csv

  report_in70s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath pfizer all
    needs: [design, models_in70s_coviddeath_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/coviddeath/pfizer/all/*.svg
        tables: output/in70s/coviddeath/pfizer/all/*.csv

## az vaccine

  models_in70s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s coviddeath az all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/coviddeath/az/all/*/model*.rds
        data: output/in70s/coviddeath/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/coviddeath/az/all/*/weights*

  report_ipw_in70s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s coviddeath az all
    needs: [design, models_in70s_coviddeath_az_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/coviddeath/az/all/*/broom*.rds
        gt: output/in70s/coviddeath/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/coviddeath/az/all/*/plot*.svg
        tables: output/in70s/coviddeath/az/all/*/tab*.html
        data: output/in70s/coviddeath/az/all/*/broom*.csv

  report_in70s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath az all
    needs: [design, models_in70s_coviddeath_az_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/coviddeath/az/all/*.svg
        tables: output/in70s/coviddeath/az/all/*.csv



#######################################
 ## OVERALL MODELS: all-cause death, vax1 only (ignores second dose)
#######################################

## any vaccine

  models_in70s_death_any_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s death any all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/death/any/all/*/model*.rds
        data: output/in70s/death/any/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/death/any/all/*/weights*

  report_ipw_in70s_death_any_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s death any all
    needs: [design, models_in70s_death_any_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/death/any/all/*/broom*.rds
        gt: output/in70s/death/any/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/death/any/all/*/plot*.svg
        tables: output/in70s/death/any/all/*/tab*.html
        data: output/in70s/death/any/all/*/broom*.csv

  report_in70s_death_any_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s death any all
    needs: [design, models_in70s_death_any_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/death/any/all/*.svg
        tables: output/in70s/death/any/all/*.csv

## pfizer vaccine

  models_in70s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s death pfizer all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/death/pfizer/all/*/model*.rds
        data: output/in70s/death/pfizer/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/death/pfizer/all/*/weights*

  report_ipw_in70s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s death pfizer all
    needs: [design, models_in70s_death_pfizer_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/death/pfizer/all/*/broom*.rds
        gt: output/in70s/death/pfizer/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/death/pfizer/all/*/plot*.svg
        tables: output/in70s/death/pfizer/all/*/tab*.html
        data: output/in70s/death/pfizer/all/*/broom*.csv

  report_in70s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s death pfizer all
    needs: [design, models_in70s_death_pfizer_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/death/pfizer/all/*.svg
        tables: output/in70s/death/pfizer/all/*.csv

## az vaccine

  models_in70s_death_az_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s death az all
    needs: [design, data_stset_in70s, data_samples_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/death/az/all/*/model*.rds
        data: output/in70s/death/az/all/*/data*.rds
      moderately_sensitive:
        weights: output/in70s/death/az/all/*/weights*

  report_ipw_in70s_death_az_all:
    run: r:latest analysis/R/dose_1/report_ipw.R in70s death az all
    needs: [design, models_in70s_death_az_all]
    outputs:
      highly_sensitive:
        broom: output/in70s/death/az/all/*/broom*.rds
        gt: output/in70s/death/az/all/*/gt*.rds
      moderately_sensitive:
        plots: output/in70s/death/az/all/*/plot*.svg
        tables: output/in70s/death/az/all/*/tab*.html
        data: output/in70s/death/az/all/*/broom*.csv

  report_in70s_death_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s death az all
    needs: [design, models_in70s_death_az_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/death/az/all/*.svg
        tables: output/in70s/death/az/all/*.csv



#######################################
 ## COMBINE OVERALL MODELS:
#######################################

  # report_in70s_any_all:
  #   run: r:latest analysis/R/dose_1/report_alloutcomes.R in70s any all
  #   needs: [design, report_in70s_postest_any_all, report_in70s_covidadmitted_any_all, report_in70s_coviddeath_any_all, report_in70s_noncoviddeath_any_all, report_in70s_death_any_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/*any_all.svg
  #       tables: output/in70s/*any_all.csv
  #       html: output/in70s/*any_all.html
  #
  # report_in70s_pfizer_all:
  #   run: r:latest analysis/R/dose_1/report_alloutcomes.R in70s pfizer all
  #   needs: [design, report_in70s_postest_pfizer_all, report_in70s_covidadmitted_pfizer_all, report_in70s_coviddeath_pfizer_all, report_in70s_noncoviddeath_pfizer_all, report_in70s_death_pfizer_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/*pfizer_all.svg
  #       tables: output/in70s/*pfizer_all.csv
  #       html: output/in70s/*pfizer_all.html
  #
  # report_in70s_az_all:
  #   run: r:latest analysis/R/dose_1/report_alloutcomes.R in70s az all
  #   needs: [design, report_in70s_postest_az_all, report_in70s_covidadmitted_az_all, report_in70s_coviddeath_az_all, report_in70s_noncoviddeath_az_all, report_in70s_death_az_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/*az_all.svg
  #       tables: output/in70s/*az_all.csv
  #       html: output/in70s/*az_all.html


  report_ipw_in70s_all:
    run: r:latest analysis/R/dose_1/report_vaxmodel.R in70s death all
    needs: [design, report_ipw_in70s_death_any_all, report_ipw_in70s_death_pfizer_all, report_ipw_in70s_death_az_all]
    outputs:
      moderately_sensitive:
        svg: output/in70s/plot_vax1.svg
        #html: output/in70s/tab_vax1.html
        csv: output/in70s/tab_vax1.csv
        csv1: output/in70s/tab_vax1_wide.csv


  report_in70s_all:
    run: r:latest analysis/R/dose_1/report_alloutcomes_combined.R in70s all
    needs: [design, report_in70s_postest_any_all, report_in70s_covidadmitted_any_all, report_in70s_coviddeath_any_all, report_in70s_noncoviddeath_any_all, report_in70s_death_any_all,
    report_in70s_postest_pfizer_all, report_in70s_covidadmitted_pfizer_all, report_in70s_coviddeath_pfizer_all, report_in70s_noncoviddeath_pfizer_all, report_in70s_death_pfizer_all,
    report_in70s_postest_az_all, report_in70s_covidadmitted_az_all, report_in70s_coviddeath_az_all, report_in70s_noncoviddeath_az_all, report_in70s_death_az_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/*_all.svg
        plots1: output/in70s/*_all.png
        tables: output/in70s/*_all.csv


#### combine #####

  descr_events_combine:
    run: r:latest analysis/R/descr_events_all.R
    needs: [design, descr_events_over80s, descr_events_in70s]
    outputs:
      moderately_sensitive:
        plots: output/*.svg
        plots2: output/*.png

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 01:53:36

Config

  • Backend:
    TPP
  • Workspace:
    covid-vaccine-effectiveness-research_main
  • Branch:
    main
  • Creator:
    wjchulme
  • Force run dependencies:
    False
  • Git Commit Hash:
    4526dfa
  • Requested actions:
    • design
    • models_over80s_postest_any_immuno
    • report_ipw_over80s_postest_any_immuno
    • report_over80s_postest_any_immuno