project.yaml

version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create-project.R 
  ## Edit and run create-project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##   
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  ## PRELIIMINARIES 
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  ##  
  ## `design` defines study metadata: 

  design:
    run: r:latest analysis/design.R
    outputs:
      moderately_sensitive:
        lib: lib/design/study-dates.json

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## SEQUENTIAL TRIAL APPROACH 
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  ##  
  ## `extract_treated` extracts data from individuals who received a 
  ## vaccine dose during the study recruitment period: 

  extract_treated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_treated
      --output-file output/sequential/treated/extract/input_treated.feather
    needs:
    - design
    - process_single
    outputs:
      highly_sensitive:
        extract: output/sequential/treated/extract/input_treated.feather

  ## `process_treated` processes data and apply eligibility criteria: 

  process_treated:
    run: r:latest analysis/process/process_data.R treated
    needs:
    - extract_treated
    outputs:
      highly_sensitive:
        eligible: output/sequential/treated/eligible/*.rds
        pfizer: output/sequential/pfizer/treated/*.rds
        az: output/sequential/az/treated/*.rds
      moderately_sensitive:
        eligiblecsv: output/sequential/treated/eligible/*.csv
        input_treated_skim: output/sequential/treated/extract/*.txt
        data_processed_skim: output/sequential/treated/process/*.txt
        data_eligible_skim: output/sequential/treated/eligible/*.txt

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Extract control data, match and model for the pfizer trials 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
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  ##  
  ## Due to constraints in the way that data are extracted using the 
  ## opensafely cohort extractor (i.e. one-row-per-patient), we 
  ## conduct the matching over 4 rounds. Each round (denoted  
  ## {matching_round}) implements the following actions: 
  ##  
  ## - `extract_controlpotential_pfizer_{matching_round}` extracts data 
  ##   from individuals who are potential controls for matching in  
  ##   matching round {matching_round} 
  ##  
  ## - `process_controlpotential_pfizer_{matching_round}` processes the 
  ##   extracted data and applies the eligibility criteria 
  ##  
  ## - `match_potential_pfizer_{matching_round}` matches the potential 
  ##   controls the the treated individuals 
  ##  
  ## - `extract_controlactual_pfizer_{matching_round}` re-extracts data 
  ##   from the individuals who were matched as controls in 
  ##   `match_potential_pfizer_{matching_round}`, with data re-defined 
  ##   on `trial_date` (the start date fo the sequential trial to which 
  ##   they were assigned) 
  ##  
  ## - `process_controlactual_pfizer_{matching_round}` processes the 
  ##   data extracted in `extract_controlactual_pfizer_{matching_round}` 
  ##   and checks that the matches made in 
  ##   `match_potential_pfizer_{matching_round}` still match bases on 
  ##   the re-extracted data 
  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 1: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_pfizer_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/pfizer/matchround1/extract/input_controlpotential.feather
      --param brand=pfizer --param matching_round=1 --param index_date=2020-12-08
    needs:
    - design
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround1/extract/input_controlpotential.feather

  process_controlpotential_pfizer_1:
    run: r:latest analysis/process/process_data.R potential pfizer 1
    needs:
    - extract_controlpotential_pfizer_1
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround1/process/*.rds
        csv: output/sequential/pfizer/matchround1/process/*.csv.gz
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/pfizer/matchround1/extract/potential/*.txt
        data_processed_skim: output/sequential/pfizer/matchround1/potential/*.txt
        data_controlpotential_skim: output/sequential/pfizer/matchround1/process/*.txt

  match_potential_pfizer_1:
    run: r:latest analysis/sequential/matching/match_potential.R pfizer 1
    needs:
    - process_treated
    - process_controlpotential_pfizer_1
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround1/potential/*.rds
        csv: output/sequential/pfizer/matchround1/potential/*.csv.gz

  extract_controlactual_pfizer_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/pfizer/matchround1/extract/input_controlactual.feather
      --param brand=pfizer --param matching_round=1
    needs:
    - design
    - match_potential_pfizer_1
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround1/extract/input_controlactual.feather

  process_controlactual_pfizer_1:
    run: r:latest analysis/process/process_data.R actual pfizer 1
    needs:
    - process_treated
    - match_potential_pfizer_1
    - extract_controlpotential_pfizer_1
    - process_controlpotential_pfizer_1
    - extract_controlactual_pfizer_1
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround1/actual/*.rds
        csv: output/sequential/pfizer/matchround1/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/pfizer/matchround1/extract/actual/*.txt
        data_actual_skim: output/sequential/pfizer/matchround1/actual/*.txt

  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 2: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_pfizer_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/pfizer/matchround2/extract/input_controlpotential.feather
      --param brand=pfizer --param matching_round=2 --param index_date=2020-12-22
    needs:
    - design
    - process_single
    - process_controlactual_pfizer_1
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround2/extract/input_controlpotential.feather

  process_controlpotential_pfizer_2:
    run: r:latest analysis/process/process_data.R potential pfizer 2
    needs:
    - extract_controlpotential_pfizer_2
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround2/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/pfizer/matchround2/extract/potential/*.txt
        data_processed_skim: output/sequential/pfizer/matchround2/potential/*.txt
        data_controlpotential_skim: output/sequential/pfizer/matchround2/process/*.txt

  match_potential_pfizer_2:
    run: r:latest analysis/sequential/matching/match_potential.R pfizer 2
    needs:
    - process_treated
    - process_controlpotential_pfizer_2
    - process_controlactual_pfizer_1
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround2/potential/*.rds
        csv: output/sequential/pfizer/matchround2/potential/*.csv.gz

  extract_controlactual_pfizer_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/pfizer/matchround2/extract/input_controlactual.feather
      --param brand=pfizer --param matching_round=2
    needs:
    - design
    - match_potential_pfizer_2
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround2/extract/input_controlactual.feather

  process_controlactual_pfizer_2:
    run: r:latest analysis/process/process_data.R actual pfizer 2
    needs:
    - process_treated
    - match_potential_pfizer_2
    - extract_controlpotential_pfizer_2
    - process_controlpotential_pfizer_2
    - extract_controlactual_pfizer_2
    - process_controlactual_pfizer_1
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround2/actual/*.rds
        csv: output/sequential/pfizer/matchround2/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/pfizer/matchround2/extract/actual/*.txt
        data_actual_skim: output/sequential/pfizer/matchround2/actual/*.txt

  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 3: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_pfizer_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/pfizer/matchround3/extract/input_controlpotential.feather
      --param brand=pfizer --param matching_round=3 --param index_date=2021-01-05
    needs:
    - design
    - process_single
    - process_controlactual_pfizer_2
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround3/extract/input_controlpotential.feather

  process_controlpotential_pfizer_3:
    run: r:latest analysis/process/process_data.R potential pfizer 3
    needs:
    - extract_controlpotential_pfizer_3
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround3/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/pfizer/matchround3/extract/potential/*.txt
        data_processed_skim: output/sequential/pfizer/matchround3/potential/*.txt
        data_controlpotential_skim: output/sequential/pfizer/matchround3/process/*.txt

  match_potential_pfizer_3:
    run: r:latest analysis/sequential/matching/match_potential.R pfizer 3
    needs:
    - process_treated
    - process_controlpotential_pfizer_3
    - process_controlactual_pfizer_2
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround3/potential/*.rds
        csv: output/sequential/pfizer/matchround3/potential/*.csv.gz

  extract_controlactual_pfizer_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/pfizer/matchround3/extract/input_controlactual.feather
      --param brand=pfizer --param matching_round=3
    needs:
    - design
    - match_potential_pfizer_3
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround3/extract/input_controlactual.feather

  process_controlactual_pfizer_3:
    run: r:latest analysis/process/process_data.R actual pfizer 3
    needs:
    - process_treated
    - match_potential_pfizer_3
    - extract_controlpotential_pfizer_3
    - process_controlpotential_pfizer_3
    - extract_controlactual_pfizer_3
    - process_controlactual_pfizer_2
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround3/actual/*.rds
        csv: output/sequential/pfizer/matchround3/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/pfizer/matchround3/extract/actual/*.txt
        data_actual_skim: output/sequential/pfizer/matchround3/actual/*.txt

  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 4: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_pfizer_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/pfizer/matchround4/extract/input_controlpotential.feather
      --param brand=pfizer --param matching_round=4 --param index_date=2021-01-19
    needs:
    - design
    - process_single
    - process_controlactual_pfizer_3
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround4/extract/input_controlpotential.feather

  process_controlpotential_pfizer_4:
    run: r:latest analysis/process/process_data.R potential pfizer 4
    needs:
    - extract_controlpotential_pfizer_4
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround4/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/pfizer/matchround4/extract/potential/*.txt
        data_processed_skim: output/sequential/pfizer/matchround4/potential/*.txt
        data_controlpotential_skim: output/sequential/pfizer/matchround4/process/*.txt

  match_potential_pfizer_4:
    run: r:latest analysis/sequential/matching/match_potential.R pfizer 4
    needs:
    - process_treated
    - process_controlpotential_pfizer_4
    - process_controlactual_pfizer_3
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround4/potential/*.rds
        csv: output/sequential/pfizer/matchround4/potential/*.csv.gz

  extract_controlactual_pfizer_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/pfizer/matchround4/extract/input_controlactual.feather
      --param brand=pfizer --param matching_round=4
    needs:
    - design
    - match_potential_pfizer_4
    outputs:
      highly_sensitive:
        cohort: output/sequential/pfizer/matchround4/extract/input_controlactual.feather

  process_controlactual_pfizer_4:
    run: r:latest analysis/process/process_data.R actual pfizer 4
    needs:
    - process_treated
    - match_potential_pfizer_4
    - extract_controlpotential_pfizer_4
    - process_controlpotential_pfizer_4
    - extract_controlactual_pfizer_4
    - process_controlactual_pfizer_3
    outputs:
      highly_sensitive:
        rds: output/sequential/pfizer/matchround4/actual/*.rds
        csv: output/sequential/pfizer/matchround4/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/pfizer/matchround4/extract/actual/*.txt
        data_actual_skim: output/sequential/pfizer/matchround4/actual/*.txt

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Extract and process data from final controls in the pfizer trials 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## `extract_controlfinal_pfizer` extracts data from successful matches 
  ## across all matching rounds: 

  extract_controlfinal_pfizer:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlfinal
      --output-file output/sequential/pfizer/extract/input_controlfinal.feather --param
      brand=pfizer --param n_matching_rounds=4
    needs:
    - design
    - process_controlactual_pfizer_4
    outputs:
      highly_sensitive:
        extract: output/sequential/pfizer/extract/input_controlfinal.feather

  ## `dummydata_controlfinal_pfizer` creates dummy data to represent 
  ## the dummy data extraced in `extract_controlfinal_pfizer`(for  
  ## testing only): 

  dummydata_controlfinal_pfizer:
    run: r:latest analysis/dummy/dummydata_controlfinal.R pfizer
    needs:
    - process_controlactual_pfizer_1
    - process_controlactual_pfizer_2
    - process_controlactual_pfizer_3
    - process_controlactual_pfizer_4
    outputs:
      highly_sensitive:
        dummydata_controlfinal: output/sequential/pfizer/dummydata/dummy_control_final.feather

  ## `process_controlfinal_pfizer` processes the data extracted in 
  ## extract_controlfinal_pfizer: 

  process_controlfinal_pfizer:
    run: r:latest analysis/process/process_data.R final pfizer
    needs:
    - process_controlactual_pfizer_1
    - process_controlactual_pfizer_2
    - process_controlactual_pfizer_3
    - process_controlactual_pfizer_4
    - extract_controlfinal_pfizer
    - process_treated
    - dummydata_controlfinal_pfizer
    outputs:
      highly_sensitive:
        extract: output/sequential/pfizer/match/*.rds
      moderately_sensitive:
        input_controlfinal_skim: output/sequential/pfizer/extract/*.txt
        data_matched_skim: output/sequential/pfizer/match/*.txt

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## pfizer trial summary 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## `coverage_pfizer` summarises the matching coverage on each day of 
  ## the recruitment period: 

  coverage_pfizer:
    run: r:latest analysis/sequential/matching/coverage.R pfizer
    needs:
    - process_treated
    - process_controlfinal_pfizer
    outputs:
      moderately_sensitive:
        coverage: output/report/coverage/coverage_pfizer.csv

  ## `table1_sequential_pfizer` summarises matching variables and 
  ## baseline covariates for individuals included in the pfizer trials: 

  table1_sequential_pfizer:
    run: r:latest analysis/report/table1.R sequential pfizer
    needs:
    - process_treated
    - process_controlfinal_pfizer
    outputs:
      moderately_sensitive:
        table1: output/report/table1/table1_sequential_pfizer_rounded.csv

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Fit models to the sequential trials data 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## `kmcox_pfizer_{subgroup}_{outcome}` actions fit models to the 
  ## pfizer trial data for a given {subgroup} and {outcome}: 

  kmcox_pfizer_all_postest:
    run: r:latest analysis/sequential/model/kmcox.R pfizer all postest
    needs:
    - process_controlfinal_pfizer
    outputs:
      moderately_sensitive:
        rds: output/sequential/pfizer/model/all/postest/*.rds
        png: output/sequential/pfizer/model/all/postest/*.png

  kmcox_pfizer_all_covidadmitted:
    run: r:latest analysis/sequential/model/kmcox.R pfizer all covidadmitted
    needs:
    - process_controlfinal_pfizer
    outputs:
      moderately_sensitive:
        rds: output/sequential/pfizer/model/all/covidadmitted/*.rds
        png: output/sequential/pfizer/model/all/covidadmitted/*.png

  kmcox_pfizer_all_death:
    run: r:latest analysis/sequential/model/kmcox.R pfizer all death
    needs:
    - process_controlfinal_pfizer
    outputs:
      moderately_sensitive:
        rds: output/sequential/pfizer/model/all/death/*.rds
        png: output/sequential/pfizer/model/all/death/*.png

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Extract control data, match and model for the az trials 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## See comment at the start of the pfizer matching round for a 
  ## description of the actions in the matching round section. 
  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 1: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_az_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/az/matchround1/extract/input_controlpotential.feather
      --param brand=az --param matching_round=1 --param index_date=2021-01-04
    needs:
    - design
    - process_single
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround1/extract/input_controlpotential.feather

  process_controlpotential_az_1:
    run: r:latest analysis/process/process_data.R potential az 1
    needs:
    - extract_controlpotential_az_1
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround1/process/*.rds
        csv: output/sequential/az/matchround1/process/*.csv.gz
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/az/matchround1/extract/potential/*.txt
        data_processed_skim: output/sequential/az/matchround1/potential/*.txt
        data_controlpotential_skim: output/sequential/az/matchround1/process/*.txt

  match_potential_az_1:
    run: r:latest analysis/sequential/matching/match_potential.R az 1
    needs:
    - process_treated
    - process_controlpotential_az_1
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround1/potential/*.rds
        csv: output/sequential/az/matchround1/potential/*.csv.gz

  extract_controlactual_az_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/az/matchround1/extract/input_controlactual.feather
      --param brand=az --param matching_round=1
    needs:
    - design
    - match_potential_az_1
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround1/extract/input_controlactual.feather

  process_controlactual_az_1:
    run: r:latest analysis/process/process_data.R actual az 1
    needs:
    - process_treated
    - match_potential_az_1
    - extract_controlpotential_az_1
    - process_controlpotential_az_1
    - extract_controlactual_az_1
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround1/actual/*.rds
        csv: output/sequential/az/matchround1/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/az/matchround1/extract/actual/*.txt
        data_actual_skim: output/sequential/az/matchround1/actual/*.txt

  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 2: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_az_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/az/matchround2/extract/input_controlpotential.feather
      --param brand=az --param matching_round=2 --param index_date=2021-01-18
    needs:
    - design
    - process_single
    - process_controlactual_az_1
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround2/extract/input_controlpotential.feather

  process_controlpotential_az_2:
    run: r:latest analysis/process/process_data.R potential az 2
    needs:
    - extract_controlpotential_az_2
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround2/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/az/matchround2/extract/potential/*.txt
        data_processed_skim: output/sequential/az/matchround2/potential/*.txt
        data_controlpotential_skim: output/sequential/az/matchround2/process/*.txt

  match_potential_az_2:
    run: r:latest analysis/sequential/matching/match_potential.R az 2
    needs:
    - process_treated
    - process_controlpotential_az_2
    - process_controlactual_az_1
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround2/potential/*.rds
        csv: output/sequential/az/matchround2/potential/*.csv.gz

  extract_controlactual_az_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/az/matchround2/extract/input_controlactual.feather
      --param brand=az --param matching_round=2
    needs:
    - design
    - match_potential_az_2
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround2/extract/input_controlactual.feather

  process_controlactual_az_2:
    run: r:latest analysis/process/process_data.R actual az 2
    needs:
    - process_treated
    - match_potential_az_2
    - extract_controlpotential_az_2
    - process_controlpotential_az_2
    - extract_controlactual_az_2
    - process_controlactual_az_1
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround2/actual/*.rds
        csv: output/sequential/az/matchround2/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/az/matchround2/extract/actual/*.txt
        data_actual_skim: output/sequential/az/matchround2/actual/*.txt

  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 3: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_az_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/az/matchround3/extract/input_controlpotential.feather
      --param brand=az --param matching_round=3 --param index_date=2021-02-01
    needs:
    - design
    - process_single
    - process_controlactual_az_2
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround3/extract/input_controlpotential.feather

  process_controlpotential_az_3:
    run: r:latest analysis/process/process_data.R potential az 3
    needs:
    - extract_controlpotential_az_3
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround3/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/az/matchround3/extract/potential/*.txt
        data_processed_skim: output/sequential/az/matchround3/potential/*.txt
        data_controlpotential_skim: output/sequential/az/matchround3/process/*.txt

  match_potential_az_3:
    run: r:latest analysis/sequential/matching/match_potential.R az 3
    needs:
    - process_treated
    - process_controlpotential_az_3
    - process_controlactual_az_2
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround3/potential/*.rds
        csv: output/sequential/az/matchround3/potential/*.csv.gz

  extract_controlactual_az_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/az/matchround3/extract/input_controlactual.feather
      --param brand=az --param matching_round=3
    needs:
    - design
    - match_potential_az_3
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround3/extract/input_controlactual.feather

  process_controlactual_az_3:
    run: r:latest analysis/process/process_data.R actual az 3
    needs:
    - process_treated
    - match_potential_az_3
    - extract_controlpotential_az_3
    - process_controlpotential_az_3
    - extract_controlactual_az_3
    - process_controlactual_az_2
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround3/actual/*.rds
        csv: output/sequential/az/matchround3/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/az/matchround3/extract/actual/*.txt
        data_actual_skim: output/sequential/az/matchround3/actual/*.txt

  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Matching round 4: 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  extract_controlpotential_az_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
      --output-file output/sequential/az/matchround4/extract/input_controlpotential.feather
      --param brand=az --param matching_round=4 --param index_date=2021-02-15
    needs:
    - design
    - process_single
    - process_controlactual_az_3
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround4/extract/input_controlpotential.feather

  process_controlpotential_az_4:
    run: r:latest analysis/process/process_data.R potential az 4
    needs:
    - extract_controlpotential_az_4
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround4/process/*.rds
      moderately_sensitive:
        input_controlpotential_skim: output/sequential/az/matchround4/extract/potential/*.txt
        data_processed_skim: output/sequential/az/matchround4/potential/*.txt
        data_controlpotential_skim: output/sequential/az/matchround4/process/*.txt

  match_potential_az_4:
    run: r:latest analysis/sequential/matching/match_potential.R az 4
    needs:
    - process_treated
    - process_controlpotential_az_4
    - process_controlactual_az_3
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround4/potential/*.rds
        csv: output/sequential/az/matchround4/potential/*.csv.gz

  extract_controlactual_az_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
      --output-file output/sequential/az/matchround4/extract/input_controlactual.feather
      --param brand=az --param matching_round=4
    needs:
    - design
    - match_potential_az_4
    outputs:
      highly_sensitive:
        cohort: output/sequential/az/matchround4/extract/input_controlactual.feather

  process_controlactual_az_4:
    run: r:latest analysis/process/process_data.R actual az 4
    needs:
    - process_treated
    - match_potential_az_4
    - extract_controlpotential_az_4
    - process_controlpotential_az_4
    - extract_controlactual_az_4
    - process_controlactual_az_3
    outputs:
      highly_sensitive:
        rds: output/sequential/az/matchround4/actual/*.rds
        csv: output/sequential/az/matchround4/actual/*.csv.gz
      moderately_sensitive:
        input_controlactual_skim: output/sequential/az/matchround4/extract/actual/*.txt
        data_actual_skim: output/sequential/az/matchround4/actual/*.txt

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Extract and process data from final controls in the az trials 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## `extract_controlfinal_az` extracts data from successful matches 
  ## across all matching rounds: 

  extract_controlfinal_az:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_controlfinal
      --output-file output/sequential/az/extract/input_controlfinal.feather --param
      brand=az --param n_matching_rounds=4
    needs:
    - design
    - process_controlactual_az_4
    outputs:
      highly_sensitive:
        extract: output/sequential/az/extract/input_controlfinal.feather

  ## `dummydata_controlfinal_az` creates dummy data to represent 
  ## the dummy data extraced in `extract_controlfinal_az`(for  
  ## testing only): 

  dummydata_controlfinal_az:
    run: r:latest analysis/dummy/dummydata_controlfinal.R az
    needs:
    - process_controlactual_az_1
    - process_controlactual_az_2
    - process_controlactual_az_3
    - process_controlactual_az_4
    outputs:
      highly_sensitive:
        dummydata_controlfinal: output/sequential/az/dummydata/dummy_control_final.feather

  ## `process_controlfinal_az` processes the data extracted in 
  ## extract_controlfinal_az: 

  process_controlfinal_az:
    run: r:latest analysis/process/process_data.R final az
    needs:
    - process_controlactual_az_1
    - process_controlactual_az_2
    - process_controlactual_az_3
    - process_controlactual_az_4
    - extract_controlfinal_az
    - process_treated
    - dummydata_controlfinal_az
    outputs:
      highly_sensitive:
        extract: output/sequential/az/match/*.rds
      moderately_sensitive:
        input_controlfinal_skim: output/sequential/az/extract/*.txt
        data_matched_skim: output/sequential/az/match/*.txt

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## az trial summary 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## `coverage_az` summarises the matching coverage on each day of 
  ## the recruitment period: 

  coverage_az:
    run: r:latest analysis/sequential/matching/coverage.R az
    needs:
    - process_treated
    - process_controlfinal_az
    outputs:
      moderately_sensitive:
        coverage: output/report/coverage/coverage_az.csv

  ## `table1_sequential_az` summarises matching variables and 
  ## baseline covariates for individuals included in the az trials: 

  table1_sequential_az:
    run: r:latest analysis/report/table1.R sequential az
    needs:
    - process_treated
    - process_controlfinal_az
    outputs:
      moderately_sensitive:
        table1: output/report/table1/table1_sequential_az_rounded.csv

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Fit models to the sequential trials data 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## `kmcox_pfizer_{subgroup}_{outcome}` actions fit models to the 
  ## az trial data for a given {subgroup} and {outcome}: 

  kmcox_az_all_postest:
    run: r:latest analysis/sequential/model/kmcox.R az all postest
    needs:
    - process_controlfinal_az
    outputs:
      moderately_sensitive:
        rds: output/sequential/az/model/all/postest/*.rds
        png: output/sequential/az/model/all/postest/*.png

  kmcox_az_all_covidadmitted:
    run: r:latest analysis/sequential/model/kmcox.R az all covidadmitted
    needs:
    - process_controlfinal_az
    outputs:
      moderately_sensitive:
        rds: output/sequential/az/model/all/covidadmitted/*.rds
        png: output/sequential/az/model/all/covidadmitted/*.png

  kmcox_az_all_death:
    run: r:latest analysis/sequential/model/kmcox.R az all death
    needs:
    - process_controlfinal_az
    outputs:
      moderately_sensitive:
        rds: output/sequential/az/model/all/death/*.rds
        png: output/sequential/az/model/all/death/*.png

  ## `combine_kmcox` combines output from all actions that run `kmcox.R`: 

  combine_kmcox:
    run: r:latest analysis/sequential/model/kmcox_combine.R
    needs:
    - kmcox_pfizer_all_postest
    - kmcox_pfizer_all_covidadmitted
    - kmcox_pfizer_all_death
    - kmcox_az_all_postest
    - kmcox_az_all_covidadmitted
    - kmcox_az_all_death
    outputs:
      moderately_sensitive:
        rds: output/sequential/combine/*.csv
        png: output/sequential/combine/*.png

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## SINGLE TRIAL APPROACH 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Extract and process data 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## `process_single` processes data extracted in the  
  ## `extract_controlpotential_pfizer_1` action for the 
  ## single trial approach: 

  process_single:
    run: r:latest analysis/process/process_data.R single
    needs:
    - extract_controlpotential_pfizer_1
    outputs:
      highly_sensitive:
        eligible: output/single/eligible/*.rds
      moderately_sensitive:
        eligiblecsv: output/single/eligible/*.csv
        eligiblecsvgz: output/single/eligible/*.csv.gz
        data_processed_skim: output/single/process/*.txt
        data_eligible_skim: output/single/eligible/*.txt

  ## `table1_single_any` calculates summary statistics for the single 
  ## trial cohort: 

  table1_single_any:
    run: r:latest analysis/report/table1.R single any
    needs:
    - process_single
    outputs:
      moderately_sensitive:
        table1: output/report/table1/table1_single_any_rounded.csv

  ## `extract_timevarying` extracts the data needed to derive 
  ## time-varying covariates and outcome variables for the single trial 
  ## approach: 

  extract_timevarying:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_timevarying
      --output-file output/single/extract/input_timevarying.feather
    needs:
    - design
    - process_single
    outputs:
      highly_sensitive:
        extract: output/single/extract/input_timevarying.feather

  ## `dummydata_timevarying` creates dummy data represent the data 
  ## extracted in `extract_timevarying` (for testing only): 

  dummydata_timevarying:
    run: r:latest analysis/dummy/dummydata_timevarying.R
    needs:
    - process_single
    - extract_timevarying
    outputs:
      highly_sensitive:
        dummydata: output/single/dummydata/*.feather

  ## `process_timevarying` processes the data extracted in  
  ## `extract_timevarying` to create time-varying covariates and outcome 
  ## variables: 

  process_timevarying:
    run: r:latest analysis/single/process/process_timevarying.R
    needs:
    - process_single
    - extract_timevarying
    - dummydata_timevarying
    outputs:
      highly_sensitive:
        processed: output/single/process/*.rds

  ## `process_stset` creates time-to-event datasets necessary to derive 
  ## data_days (one-row-per-patient-per-day): 

  process_stset:
    run: r:latest analysis/single/process/process_stset.R
    needs:
    - process_single
    - process_timevarying
    outputs:
      highly_sensitive:
        processed: output/single/stset/*.rds

  ## `process_data_days` creates a one-row-per-patient-per-day dataset; 
  ## this is split across `process_data_days_n` defined in 
  ## due to memory constraints: 

  process_data_days:
    run: r:latest analysis/single/process/process_data_days.R
    needs:
    - process_stset
    outputs:
      highly_sensitive:
        processed: output/single/stset/data_days_*.rds

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Fit models to the single trials data 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## The actions in this section do the following: 
  ##  
  ## - `preflight_{brand}_{subgroup}_{outcome}_{stage} 
  ##   checks for separation between covariates and outcomes 
  ##  
  ## - `ipw_{brand}_{subgroup}_{outcome} fits models to calculate the 
  ##   probability of vaccination models 
  ##  
  ## - `msm_{brand}_{subgroup}_{outcome} fits marginal structural models 
  ##    to predict the odds of outcome events 
  ##  
  ## - `postprocess_{brand}_{subgroup}_{outcome}` processes the 
  ##   output from the `ipw_preflight_{brand}_{subgroup}_{outcome}` 
  ##   and `msm_preflight_{brand}_{subgroup}_{outcome}` actions 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Model: brand = pfizer; subgroup = all; outcome = postest 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  preflight_pfizer_all_postest_vaccine:
    run: r:latest analysis/single/model/preflight.R pfizer all postest vaccine
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/pfizer/all/postest/preflight/vaccine/*.csv
        html: output/single/pfizer/all/postest/preflight/vaccine/*.html

  preflight_pfizer_all_postest_outcome:
    run: r:latest analysis/single/model/preflight.R pfizer all postest outcome
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/pfizer/all/postest/preflight/outcome/*.csv
        html: output/single/pfizer/all/postest/preflight/outcome/*.html

  ipw_pfizer_all_postest:
    run: r:latest analysis/single/model/ipw.R pfizer all postest
    needs:
    - process_stset
    - process_data_days
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/postest/ipw/*.rds
      moderately_sensitive:
        svg: output/single/pfizer/all/postest/ipw/*.svg
        txt: output/single/pfizer/all/postest/ipw/*.txt

  msm_pfizer_all_postest:
    run: r:latest analysis/single/model/msm.R pfizer all postest
    needs:
    - ipw_pfizer_all_postest
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/postest/msm/*.rds
      moderately_sensitive:
        csv: output/single/pfizer/all/postest/msm/*.csv

  postprocess_pfizer_all_postest:
    run: r:latest analysis/single/model/postprocess.R pfizer all postest
    needs:
    - ipw_pfizer_all_postest
    - msm_pfizer_all_postest
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/postest/postprocess/*.rds
      moderately_sensitive:
        csv: output/single/pfizer/all/postest/postprocess/*.csv
        svg: output/single/pfizer/all/postest/postprocess/*.svg

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Model: brand = pfizer; subgroup = all; outcome = covidadmitted 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  preflight_pfizer_all_covidadmitted_vaccine:
    run: r:latest analysis/single/model/preflight.R pfizer all covidadmitted vaccine
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/pfizer/all/covidadmitted/preflight/vaccine/*.csv
        html: output/single/pfizer/all/covidadmitted/preflight/vaccine/*.html

  preflight_pfizer_all_covidadmitted_outcome:
    run: r:latest analysis/single/model/preflight.R pfizer all covidadmitted outcome
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/pfizer/all/covidadmitted/preflight/outcome/*.csv
        html: output/single/pfizer/all/covidadmitted/preflight/outcome/*.html

  ipw_pfizer_all_covidadmitted:
    run: r:latest analysis/single/model/ipw.R pfizer all covidadmitted
    needs:
    - process_stset
    - process_data_days
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/covidadmitted/ipw/*.rds
      moderately_sensitive:
        svg: output/single/pfizer/all/covidadmitted/ipw/*.svg
        txt: output/single/pfizer/all/covidadmitted/ipw/*.txt

  msm_pfizer_all_covidadmitted:
    run: r:latest analysis/single/model/msm.R pfizer all covidadmitted
    needs:
    - ipw_pfizer_all_covidadmitted
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/covidadmitted/msm/*.rds
      moderately_sensitive:
        csv: output/single/pfizer/all/covidadmitted/msm/*.csv

  postprocess_pfizer_all_covidadmitted:
    run: r:latest analysis/single/model/postprocess.R pfizer all covidadmitted
    needs:
    - ipw_pfizer_all_covidadmitted
    - msm_pfizer_all_covidadmitted
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/covidadmitted/postprocess/*.rds
      moderately_sensitive:
        csv: output/single/pfizer/all/covidadmitted/postprocess/*.csv
        svg: output/single/pfizer/all/covidadmitted/postprocess/*.svg

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Model: brand = pfizer; subgroup = all; outcome = death 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  preflight_pfizer_all_death_vaccine:
    run: r:latest analysis/single/model/preflight.R pfizer all death vaccine
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/pfizer/all/death/preflight/vaccine/*.csv
        html: output/single/pfizer/all/death/preflight/vaccine/*.html

  preflight_pfizer_all_death_outcome:
    run: r:latest analysis/single/model/preflight.R pfizer all death outcome
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/pfizer/all/death/preflight/outcome/*.csv
        html: output/single/pfizer/all/death/preflight/outcome/*.html

  ipw_pfizer_all_death:
    run: r:latest analysis/single/model/ipw.R pfizer all death
    needs:
    - process_stset
    - process_data_days
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/death/ipw/*.rds
      moderately_sensitive:
        svg: output/single/pfizer/all/death/ipw/*.svg
        txt: output/single/pfizer/all/death/ipw/*.txt

  msm_pfizer_all_death:
    run: r:latest analysis/single/model/msm.R pfizer all death
    needs:
    - ipw_pfizer_all_death
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/death/msm/*.rds
      moderately_sensitive:
        csv: output/single/pfizer/all/death/msm/*.csv

  postprocess_pfizer_all_death:
    run: r:latest analysis/single/model/postprocess.R pfizer all death
    needs:
    - ipw_pfizer_all_death
    - msm_pfizer_all_death
    outputs:
      highly_sensitive:
        rds: output/single/pfizer/all/death/postprocess/*.rds
      moderately_sensitive:
        csv: output/single/pfizer/all/death/postprocess/*.csv
        svg: output/single/pfizer/all/death/postprocess/*.svg

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Model: brand = az; subgroup = all; outcome = postest 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  preflight_az_all_postest_vaccine:
    run: r:latest analysis/single/model/preflight.R az all postest vaccine
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/az/all/postest/preflight/vaccine/*.csv
        html: output/single/az/all/postest/preflight/vaccine/*.html

  preflight_az_all_postest_outcome:
    run: r:latest analysis/single/model/preflight.R az all postest outcome
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/az/all/postest/preflight/outcome/*.csv
        html: output/single/az/all/postest/preflight/outcome/*.html

  ipw_az_all_postest:
    run: r:latest analysis/single/model/ipw.R az all postest
    needs:
    - process_stset
    - process_data_days
    outputs:
      highly_sensitive:
        rds: output/single/az/all/postest/ipw/*.rds
      moderately_sensitive:
        svg: output/single/az/all/postest/ipw/*.svg
        txt: output/single/az/all/postest/ipw/*.txt

  msm_az_all_postest:
    run: r:latest analysis/single/model/msm.R az all postest
    needs:
    - ipw_az_all_postest
    outputs:
      highly_sensitive:
        rds: output/single/az/all/postest/msm/*.rds
      moderately_sensitive:
        csv: output/single/az/all/postest/msm/*.csv

  postprocess_az_all_postest:
    run: r:latest analysis/single/model/postprocess.R az all postest
    needs:
    - ipw_az_all_postest
    - msm_az_all_postest
    outputs:
      highly_sensitive:
        rds: output/single/az/all/postest/postprocess/*.rds
      moderately_sensitive:
        csv: output/single/az/all/postest/postprocess/*.csv
        svg: output/single/az/all/postest/postprocess/*.svg

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Model: brand = az; subgroup = all; outcome = covidadmitted 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  preflight_az_all_covidadmitted_vaccine:
    run: r:latest analysis/single/model/preflight.R az all covidadmitted vaccine
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/az/all/covidadmitted/preflight/vaccine/*.csv
        html: output/single/az/all/covidadmitted/preflight/vaccine/*.html

  preflight_az_all_covidadmitted_outcome:
    run: r:latest analysis/single/model/preflight.R az all covidadmitted outcome
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/az/all/covidadmitted/preflight/outcome/*.csv
        html: output/single/az/all/covidadmitted/preflight/outcome/*.html

  ipw_az_all_covidadmitted:
    run: r:latest analysis/single/model/ipw.R az all covidadmitted
    needs:
    - process_stset
    - process_data_days
    outputs:
      highly_sensitive:
        rds: output/single/az/all/covidadmitted/ipw/*.rds
      moderately_sensitive:
        svg: output/single/az/all/covidadmitted/ipw/*.svg
        txt: output/single/az/all/covidadmitted/ipw/*.txt

  msm_az_all_covidadmitted:
    run: r:latest analysis/single/model/msm.R az all covidadmitted
    needs:
    - ipw_az_all_covidadmitted
    outputs:
      highly_sensitive:
        rds: output/single/az/all/covidadmitted/msm/*.rds
      moderately_sensitive:
        csv: output/single/az/all/covidadmitted/msm/*.csv

  postprocess_az_all_covidadmitted:
    run: r:latest analysis/single/model/postprocess.R az all covidadmitted
    needs:
    - ipw_az_all_covidadmitted
    - msm_az_all_covidadmitted
    outputs:
      highly_sensitive:
        rds: output/single/az/all/covidadmitted/postprocess/*.rds
      moderately_sensitive:
        csv: output/single/az/all/covidadmitted/postprocess/*.csv
        svg: output/single/az/all/covidadmitted/postprocess/*.svg

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Model: brand = az; subgroup = all; outcome = death 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  preflight_az_all_death_vaccine:
    run: r:latest analysis/single/model/preflight.R az all death vaccine
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/az/all/death/preflight/vaccine/*.csv
        html: output/single/az/all/death/preflight/vaccine/*.html

  preflight_az_all_death_outcome:
    run: r:latest analysis/single/model/preflight.R az all death outcome
    needs:
    - process_stset
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/single/az/all/death/preflight/outcome/*.csv
        html: output/single/az/all/death/preflight/outcome/*.html

  ipw_az_all_death:
    run: r:latest analysis/single/model/ipw.R az all death
    needs:
    - process_stset
    - process_data_days
    outputs:
      highly_sensitive:
        rds: output/single/az/all/death/ipw/*.rds
      moderately_sensitive:
        svg: output/single/az/all/death/ipw/*.svg
        txt: output/single/az/all/death/ipw/*.txt

  msm_az_all_death:
    run: r:latest analysis/single/model/msm.R az all death
    needs:
    - ipw_az_all_death
    outputs:
      highly_sensitive:
        rds: output/single/az/all/death/msm/*.rds
      moderately_sensitive:
        csv: output/single/az/all/death/msm/*.csv

  postprocess_az_all_death:
    run: r:latest analysis/single/model/postprocess.R az all death
    needs:
    - ipw_az_all_death
    - msm_az_all_death
    outputs:
      highly_sensitive:
        rds: output/single/az/all/death/postprocess/*.rds
      moderately_sensitive:
        csv: output/single/az/all/death/postprocess/*.csv
        svg: output/single/az/all/death/postprocess/*.svg

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## Combine model outputs 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## `msm_combine` combines the output from all actions that run `msm.R`: 

  single_combine:
    run: r:latest analysis/single/model/combine.R
    needs:
    - postprocess_pfizer_all_postest
    - postprocess_pfizer_all_covidadmitted
    - postprocess_pfizer_all_death
    - postprocess_az_all_postest
    - postprocess_az_all_covidadmitted
    - postprocess_az_all_death
    outputs:
      moderately_sensitive:
        csv: output/single/combine/*.csv
        svg: output/single/combine/*.svg

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## REPORT 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ##  
  ## `flowchart` prepares the data to be used in the particiant flow 
  ## diagram in the paper (Supplementary Figure xxx): 

  flowchart:
    run: r:latest analysis/report/flowchart.R
    needs:
    - process_treated
    - process_controlfinal_pfizer
    - process_controlfinal_az
    - process_single
    outputs:
      moderately_sensitive:
        check_NAs: output/report/flowchart/*.txt
        flow_matching: output/report/flowchart/*.csv

  ## `brand12counts` plots the cumulative incidence of first and second 
  ## vaccine doses (Figure xxx): 

  brand12counts:
    run: r:latest analysis/report/brand12counts.R
    needs:
    - process_data_days
    outputs:
      moderately_sensitive:
        csv: output/report/brand12counts/*.csv
        plots: output/report/brand12counts/*.png

  output_for_release:
    run: r:latest analysis/report/output_for_release.R
    needs:
    - table1_sequential_pfizer
    - table1_sequential_az
    - table1_single_any
    - single_combine
    - combine_kmcox
    - coverage_pfizer
    - coverage_az
    - process_stset
    outputs:
      moderately_sensitive:
        csv: output/report/release/*.csv
        plots: output/report/release/*.png

  ## #### End ####