project.yaml

version: '3.0'

expectations:
  population_size: 500000

actions:

  extract_all:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-format csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_all.csv.gz

  generate_over80s_flow_chart_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_over80s_flow_chart
    outputs:
      highly_sensitive:
        cohort: output/input_over80s_flow_chart.csv

  flow_chart_over80s:
    run: r:latest -e 'rmarkdown::render("analysis/R/study_definition_over80s_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [generate_over80s_flow_chart_data]
    outputs:
      moderately_sensitive:
        html: output/study_definition_over80s_flow_chart.html

  data_process_all:
    run: r:latest analysis/R/data_process_all.R
    needs: [extract_all]
    outputs:
      highly_sensitive:
        data1: output/data/data_all.rds
        data2: output/data/data_long_vax_dates.rds
        data3: output/data/data_long_admission_dates.rds
        data4: output/data/data_long_admission_infectious_dates.rds
        data5: output/data/data_long_admission_noninfectious_dates.rds
        data6: output/data/data_long_pr_probable_covid_dates.rds
        data7: output/data/data_long_pr_suspected_covid_dates.rds
        data8: output/data/data_long_postest_dates.rds

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

  data_properties_all:
    run: r:latest analysis/R/data_properties.R output/data/data_all.rds output/data_properties
    needs: [data_process_all]
    outputs:
      moderately_sensitive:
        datasummary: output/data_properties/data_all*.txt

  data_define_cohorts:
    run: r:latest analysis/R/data_define_cohorts.R
    needs: [data_process_all]
    outputs:
      highly_sensitive:
        data: output/data/data_cohorts.rds
      moderately_sensitive:
        metadata: output/data/metadata*
        formula: output/data/list_formula.rds
        strata: output/data/list_strata.rds
        flow: output/data/flowchart*.csv


  # descr_table1_over70s:
  #   run: r:latest analysis/R/table1_lite.R over70s
  #   needs: [data_define_cohorts, data_process_all]
  #   outputs:
  #     moderately_sensitive:
  #       table1: output/over70s/descr/tables/table*

  descr_table1_over70s_baseline:
    run: r:latest analysis/R/table1_baseline.R over70s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      moderately_sensitive:
        table1: output/over70s/descr/tables/table*


  descr_events_over70s:
    run: r:latest analysis/R/plot_status_over_time_all.R over70s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      moderately_sensitive:
        plots: output/over70s/descr/plots/*.svg
        tables: output/over70s/descr/tables/*.csv




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

  data_stset_over80s:
    run: r:latest analysis/R/data_stset.R over80s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      highly_sensitive:
        data: output/over80s/data/data_*.rds

  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

  descr_table1_over80s:
    run: r:latest analysis/R/table1_lite.R over80s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      moderately_sensitive:
        table1: output/over80s/descr/tables/table*

  descr_events_over80s:
    run: r:latest analysis/R/plot_status_over_time_all.R over80s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      moderately_sensitive:
        plots: output/over80s/descr/plots/*.svg
        tables: output/over80s/descr/tables/*.csv




#######################################
 ## COX VACCINE MODELS
#######################################


  # vaxmodels_cox_over80s_all:
  #   run: r:latest analysis/R/vax/vaxmodel_cox.R over80s all
  #   needs: [data_define_cohorts, data_stset_over80s]
  #   outputs:
  #     highly_sensitive:
  #       data: output/over80s/vaccination/all/*/data_cox_sub.rds
  #       models: output/over80s/vaccination/all/*/vaxmodelcox*.rds
  #
  # vaxreport_over80s_all:
  #   run: r:latest analysis/R/vax/vaxreport_cox.R over80s all
  #   needs: [data_define_cohorts, vaxmodels_cox_over80s_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/vaccination/all/*/plot*.svg
  #       tables: output/over80s/vaccination/all/*/tab*.html
  #       data: output/over80s/vaccination/all/*/tab*.csv

#######################################
 ## 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_postest_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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

#
#   models_cox_over80s_postest_any_all_all:
#     run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all all
#     needs: [data_define_cohorts, data_stset_over80s]
#     outputs:
#       highly_sensitive:
#         models: output/over80s/postest/any/all/*/all/modelcox*.rds
#
#   report_cox_over80s_postest_any_all_all:
#     run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all all
#     needs: [data_define_cohorts, models_cox_over80s_postest_any_all_all]
#     outputs:
#       moderately_sensitive:
#         plots: output/over80s/postest/any/all/*cox_all.svg
#         tables: output/over80s/postest/any/all/*cox_all.csv
#
#   models_cox_over80s_postest_any_all_region:
#     run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all region
#     needs: [data_define_cohorts, data_stset_over80s]
#     outputs:
#       highly_sensitive:
#         models: output/over80s/postest/any/all/*/region/modelcox*.rds
#
#   report_cox_over80s_postest_any_all_region:
#     run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all region
#     needs: [data_define_cohorts, models_cox_over80s_postest_any_all_region]
#     outputs:
#       moderately_sensitive:
#         plots: output/over80s/postest/any/all/*cox_region.svg
#         tables: output/over80s/postest/any/all/*cox_region.csv
#
#   models_cox_over80s_postest_any_all_stp:
#     run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all stp
#     needs: [data_define_cohorts, data_stset_over80s]
#     outputs:
#       highly_sensitive:
#         models: output/over80s/postest/any/all/*/stp/modelcox*.rds
#
#   report_cox_over80s_postest_any_all_stp:
#     run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all stp
#     needs: [data_define_cohorts, models_cox_over80s_postest_any_all_stp]
#     outputs:
#       moderately_sensitive:
#         plots: output/over80s/postest/any/all/*cox_stp.svg
#         tables: output/over80s/postest/any/all/*cox_stp.csv
#
#   models_cox_over80s_postest_any_all_msoa:
#     run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all msoa
#     needs: [data_define_cohorts, data_stset_over80s]
#     outputs:
#       highly_sensitive:
#         models: output/over80s/postest/any/all/*/msoa/modelcox*.rds
#
#   report_cox_over80s_postest_any_all_msoa:
#     run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all msoa
#     needs: [data_define_cohorts, models_cox_over80s_postest_any_all_msoa]
#     outputs:
#       moderately_sensitive:
#         plots: output/over80s/postest/any/all/*cox_msoa.svg
#         tables: output/over80s/postest/any/all/*cox_msoa.csv
#


## pfizer vaccine

  models_over80s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s postest pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_postest_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s postest pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_postest_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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



#
# #######################################
#  ## OVERALL MODELS: emergency attendance, vax1 only (ignores second dose)
# #######################################
#
# ## any vaccine
#
#   models_over80s_emergency_any_all:
#     run: r:latest analysis/R/dose_1/model_msm.R over80s emergency any all
#     needs: [data_define_cohorts, data_stset_over80s]
#     outputs:
#       highly_sensitive:
#         models: output/over80s/emergency/any/all/*/model*.rds
#         data: output/over80s/emergency/any/all/*/data*.rds
#       moderately_sensitive:
#         weights: output/over80s/emergency/any/all/*/weights*
#
#   report_ipw_over80s_emergency_any_all:
#     run: r:latest analysis/R/dose_1/report_ipw.R over80s emergency any all
#     needs: [data_define_cohorts, models_over80s_emergency_any_all]
#     outputs:
#       highly_sensitive:
#         gt: output/over80s/emergency/any/all/*/gt*.rds
#       moderately_sensitive:
#         plots: output/over80s/emergency/any/all/*/plot*.svg
#         tables: output/over80s/emergency/any/all/*/tab*.html
#         data: output/over80s/emergency/any/all/*/tab*.csv
#
#   report_over80s_emergency_any_all:
#     run: r:latest analysis/R/dose_1/report_msm.R over80s emergency any all
#     needs: [data_define_cohorts, models_over80s_emergency_any_all]
#     outputs:
#       moderately_sensitive:
#         plots: output/over80s/emergency/any/all/*.svg
#         tables: output/over80s/emergency/any/all/*.csv


  # models_cox_over80s_emergency_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R over80s emergency any all region
  #   needs: [data_define_cohorts, data_stset_over80s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/over80s/emergency/any/all/*/region/modelcox*.rds
  #
  # report_cox_over80s_emergency_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R over80s emergency any all region
  #   needs: [data_define_cohorts, models_cox_over80s_emergency_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/emergency/any/all/*cox_region.svg
  #       tables: output/over80s/emergency/any/all/*cox_region.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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_covidadmitted_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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


  # models_cox_over80s_covidadmitted_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R over80s covidadmitted any all region
  #   needs: [data_define_cohorts, data_stset_over80s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/over80s/covidadmitted/any/all/*/region/modelcox*.rds
  #
  # report_cox_over80s_covidadmitted_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R over80s covidadmitted any all region
  #   needs: [data_define_cohorts, models_cox_over80s_covidadmitted_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/covidadmitted/any/all/*cox_region.svg
  #       tables: output/over80s/covidadmitted/any/all/*cox_region.csv



## pfizer vaccine

  models_over80s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_covidadmitted_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_covidadmitted_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted az all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_noncoviddeath_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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


  # models_cox_over80s_noncoviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R over80s noncoviddeath any all region
  #   needs: [data_define_cohorts, data_stset_over80s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/over80s/noncoviddeath/any/all/*/region/modelcox*.rds
  #
  # report_cox_over80s_noncoviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R over80s noncoviddeath any all region
  #   needs: [data_define_cohorts, models_cox_over80s_noncoviddeath_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/noncoviddeath/any/all/*cox_region.svg
  #       tables: output/over80s/noncoviddeath/any/all/*cox_region.csv



## pfizer vaccine

  models_over80s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_noncoviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_noncoviddeath_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath az all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_over80s]
    outputs:
      highly_sensitive:
        models: output/over80s/coviddeath/any/all/*/model*.rds
        data: output/over80s/coviddeath/any/all/*/data*.rds
        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: [data_define_cohorts, models_over80s_coviddeath_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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


  # models_cox_over80s_coviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R over80s coviddeath any all region
  #   needs: [data_define_cohorts, data_stset_over80s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/over80s/coviddeath/any/all/*/region/modelcox*.rds
  #
  # report_cox_over80s_coviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R over80s coviddeath any all region
  #   needs: [data_define_cohorts, models_cox_over80s_coviddeath_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/coviddeath/any/all/*cox_region.svg
  #       tables: output/over80s/coviddeath/any/all/*cox_region.csv


## pfizer vaccine

  models_over80s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_coviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_coviddeath_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath az all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_death_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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


  # models_cox_over80s_death_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R over80s death any all region
  #   needs: [data_define_cohorts, data_stset_over80s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/over80s/death/any/all/*/region/modelcox*.rds
  #
  # report_cox_over80s_death_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R over80s death any all region
  #   needs: [data_define_cohorts, models_cox_over80s_death_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/over80s/death/any/all/*cox_region.svg
  #       tables: output/over80s/death/any/all/*cox_region.csv


## pfizer vaccine

  models_over80s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R over80s death pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_death_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_over80s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R over80s death pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_death_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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




#
# #######################################
# #######################################
# ## SUBGROUPS
# #######################################
# #######################################
#
# #######################################
#  ## sex positive test, vax1 only (ignores second dose)
# #######################################
#
# ## any vaccine
# #
# #   models_over80s_postest_any_sex:
# #     run: r:latest analysis/R/dose_1/model_msm.R over80s postest any sex
# #     needs: [data_define_cohorts, data_stset_over80s]
# #     outputs:
# #       highly_sensitive:
# #         models: output/over80s/postest/any/sex/*/model*.rds
# #         data: output/over80s/postest/any/sex/*/data_weights.rds
# #         weights: output/over80s/postest/any/sex/*/weights*
# #
# #   report_over80s_postest_any_sex:
# #     run: r:latest analysis/R/dose_1/report_msm.R over80s postest any sex
# #     needs: [data_define_cohorts, models_over80s_postest_any_sex]
# #     outputs:
# #       moderately_sensitive:
# #         plots: output/over80s/postest/any/sex/*.svg
# #         tables: output/over80s/postest/any/sex/*.csv
# #
# #
# # ## pfizer vaccine
# #   models_over80s_postest_pfizer_sex:
# #     run: r:latest analysis/R/dose_1/model_msm.R over80s postest pfizer sex
# #     needs: [data_define_cohorts, data_stset_over80s]
# #     outputs:
# #       highly_sensitive:
# #         models: output/over80s/postest/pfizer/sex/*/model*.rds
# #         data: output/over80s/postest/pfizer/sex/*/data_weights.rds
# #         weights: output/over80s/postest/pfizer/sex/*/weights*
# #
# #   report_over80s_postest_pfizer_sex:
# #     run: r:latest analysis/R/dose_1/report_msm.R over80s postest pfizer sex
# #     needs: [data_define_cohorts, models_over80s_postest_pfizer_sex]
# #     outputs:
# #       moderately_sensitive:
# #         plots: output/over80s/postest/pfizer/sex/*.svg
# #         tables: output/over80s/postest/pfizer/sex/*.csv
# #
# #
# # ## az vaccine
# #
# #   models_over80s_postest_az_sex:
# #     run: r:latest analysis/R/dose_1/model_msm.R over80s postest az sex
# #     needs: [data_define_cohorts, data_stset_over80s]
# #     outputs:
# #       highly_sensitive:
# #         models: output/over80s/postest/az/sex/*/model*.rds
# #         data: output/over80s/postest/az/sex/*/data_weights.rds
# #         weights: output/over80s/postest/az/sex/*/weights*
# #
# #
# #   report_over80s_postest_az_sex:
# #     run: r:latest analysis/R/dose_1/report_msm.R over80s postest az sex
# #     needs: [data_define_cohorts, models_over80s_postest_az_sex]
# #     outputs:
# #       moderately_sensitive:
# #         plots: output/over80s/postest/az/sex/*.svg
# #         tables: output/over80s/postest/az/sex/*.csv
# #
# #
#



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

  report_over80s_any_all:
    run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s any all
    needs: [data_define_cohorts, 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: [data_define_cohorts, 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: [data_define_cohorts, 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_over80s_all:
    run: r:latest analysis/R/dose_1/report_alloutcomes_combined.R over80s all
    needs: [data_define_cohorts, 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
        tables: output/over80s/*_all.csv



  report_ipw_over80s_any_all:
    run: r:latest analysis/R/dose_1/report_allipw.R over80s any all
    needs: [data_define_cohorts, report_ipw_over80s_postest_any_all, report_ipw_over80s_covidadmitted_any_all, report_ipw_over80s_coviddeath_any_all, report_ipw_over80s_noncoviddeath_any_all, report_ipw_over80s_death_any_all]
    outputs:
      moderately_sensitive:
        svg: output/over80s/plot_vaxany1.svg
        html: output/over80s/tab_vaxany1.html

  report_ipw_over80s_pfizer_all:
    run: r:latest analysis/R/dose_1/report_allipw.R over80s pfizer all
    needs: [data_define_cohorts, report_ipw_over80s_postest_pfizer_all, report_ipw_over80s_covidadmitted_pfizer_all, report_ipw_over80s_coviddeath_pfizer_all, report_ipw_over80s_noncoviddeath_pfizer_all, report_ipw_over80s_death_pfizer_all]
    outputs:
      moderately_sensitive:
        svg: output/over80s/plot_vaxpfizer1.svg
        html: output/over80s/tab_vaxpfizer1.html

  report_ipw_over80s_az_all:
    run: r:latest analysis/R/dose_1/report_allipw.R over80s az all
    needs: [data_define_cohorts, report_ipw_over80s_postest_az_all, report_ipw_over80s_covidadmitted_az_all, report_ipw_over80s_coviddeath_az_all, report_ipw_over80s_noncoviddeath_az_all, report_ipw_over80s_death_az_all]
    outputs:
      moderately_sensitive:
        svg: output/over80s/plot_vaxaz1.svg
        html: output/over80s/tab_vaxaz1.html


  report_ipw_over80s_all:
    run: r:latest analysis/R/dose_1/report_vaxmodel.R over80s all
    needs: [data_define_cohorts, 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


##############################################################################
##############################################################################
  ## VE in over 70s (in70s)
##############################################################################
##############################################################################

  data_stset_in70s:
    run: r:latest analysis/R/data_stset.R in70s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      highly_sensitive:
        data: output/in70s/data/data_*.rds

  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

  descr_table1_in70s:
    run: r:latest analysis/R/table1_lite.R in70s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      moderately_sensitive:
        table1: output/in70s/descr/tables/table*

  descr_events_in70s:
    run: r:latest analysis/R/plot_status_over_time_all.R in70s
    needs: [data_define_cohorts, data_process_all]
    outputs:
      moderately_sensitive:
        plots: output/in70s/descr/plots/*.svg
        tables: output/in70s/descr/tables/*.csv


#######################################
 ## COX VACCINE MODELS
#######################################


  # vaxmodels_cox_in70s_all:
  #   run: r:latest analysis/R/vax/vaxmodel_cox.R in70s all
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       data: output/in70s/vaccination/all/*/data_cox_sub.rds
  #       models: output/in70s/vaccination/all/*/vaxmodelcox*.rds
  #
  # vaxreport_in70s_all:
  #   run: r:latest analysis/R/vax/vaxreport_cox.R in70s all
  #   needs: [data_define_cohorts, vaxmodels_cox_in70s_all]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/vaccination/all/*/plot*.svg
  #       tables: output/in70s/vaccination/all/*/tab*.html
  #       data: output/in70s/vaccination/all/*/tab*.csv

#######################################
 ## 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_postest_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


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

#
#   models_cox_in70s_postest_any_all_all:
#     run: r:latest analysis/R/dose_1/model_cox.R in70s postest any all all
#     needs: [data_define_cohorts, data_stset_in70s]
#     outputs:
#       highly_sensitive:
#         models: output/in70s/postest/any/all/*/all/modelcox*.rds
#
#   report_cox_in70s_postest_any_all_all:
#     run: r:latest analysis/R/dose_1/report_cox.R in70s postest any all all
#     needs: [data_define_cohorts, models_cox_in70s_postest_any_all_all]
#     outputs:
#       moderately_sensitive:
#         plots: output/in70s/postest/any/all/*cox_all.svg
#         tables: output/in70s/postest/any/all/*cox_all.csv

  # models_cox_in70s_postest_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s postest any all region
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/postest/any/all/*/region/modelcox*.rds
  #
  # report_cox_in70s_postest_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s postest any all region
  #   needs: [data_define_cohorts, models_cox_in70s_postest_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/postest/any/all/*cox_region.svg
  #       tables: output/in70s/postest/any/all/*cox_region.csv

  # models_cox_in70s_postest_any_all_stp:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s postest any all stp
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/postest/any/all/*/stp/modelcox*.rds
  #
  # report_cox_in70s_postest_any_all_stp:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s postest any all stp
  #   needs: [data_define_cohorts, models_cox_in70s_postest_any_all_stp]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/postest/any/all/*cox_stp.svg
  #       tables: output/in70s/postest/any/all/*cox_stp.csv
  #
  # models_cox_in70s_postest_any_all_msoa:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s postest any all msoa
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/postest/any/all/*/msoa/modelcox*.rds
  #
  # report_cox_in70s_postest_any_all_msoa:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s postest any all msoa
  #   needs: [data_define_cohorts, models_cox_in70s_postest_any_all_msoa]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/postest/any/all/*cox_msoa.svg
  #       tables: output/in70s/postest/any/all/*cox_msoa.csv



## pfizer vaccine

  models_in70s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s postest pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_postest_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_in70s_postest_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s postest pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_postest_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

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


#
# #######################################
#  ## OVERALL MODELS: emergency attendance, vax1 only (ignores second dose)
# #######################################
#
# ## any vaccine
#
#   models_in70s_emergency_any_all:
#     run: r:latest analysis/R/dose_1/model_msm.R in70s emergency any all
#     needs: [data_define_cohorts, data_stset_in70s]
#     outputs:
#       highly_sensitive:
#         models: output/in70s/emergency/any/all/*/model*.rds
#         data: output/in70s/emergency/any/all/*/data*.rds
#       moderately_sensitive:
#         weights: output/in70s/emergency/any/all/*/weights*
#
#   report_ipw_in70s_emergency_any_all:
#     run: r:latest analysis/R/dose_1/report_ipw.R in70s emergency any all
#     needs: [data_define_cohorts, models_in70s_emergency_any_all]
#     outputs:
#       highly_sensitive:
#         gt: output/in70s/emergency/any/all/*/gt*.rds
#       moderately_sensitive:
#         plots: output/in70s/emergency/any/all/*/plot*.svg
#         tables: output/in70s/emergency/any/all/*/tab*.html
#         data: output/in70s/emergency/any/all/*/tab*.csv
#
#   report_in70s_emergency_any_all:
#     run: r:latest analysis/R/dose_1/report_msm.R in70s emergency any all
#     needs: [data_define_cohorts, models_in70s_emergency_any_all]
#     outputs:
#       moderately_sensitive:
#         plots: output/in70s/emergency/any/all/*.svg
#         tables: output/in70s/emergency/any/all/*.csv


  # models_cox_in70s_emergency_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s emergency any all region
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/emergency/any/all/*/region/modelcox*.rds
  #
  # report_cox_in70s_emergency_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s emergency any all region
  #   needs: [data_define_cohorts, models_cox_in70s_emergency_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/emergency/any/all/*cox_region.svg
  #       tables: output/in70s/emergency/any/all/*cox_region.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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_covidadmitted_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


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


  # models_cox_in70s_covidadmitted_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s covidadmitted any all region
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/covidadmitted/any/all/*/region/modelcox*.rds
  #
  # report_cox_in70s_covidadmitted_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s covidadmitted any all region
  #   needs: [data_define_cohorts, models_cox_in70s_covidadmitted_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/covidadmitted/any/all/*cox_region.svg
  #       tables: output/in70s/covidadmitted/any/all/*cox_region.csv



## pfizer vaccine

  models_in70s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_covidadmitted_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


  report_in70s_covidadmitted_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_covidadmitted_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


  report_in70s_covidadmitted_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s covidadmitted az all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_noncoviddeath_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


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


  # models_cox_in70s_noncoviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s noncoviddeath any all region
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/noncoviddeath/any/all/*/region/modelcox*.rds
  #
  # report_cox_in70s_noncoviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s noncoviddeath any all region
  #   needs: [data_define_cohorts, models_cox_in70s_noncoviddeath_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/noncoviddeath/any/all/*cox_region.svg
  #       tables: output/in70s/noncoviddeath/any/all/*cox_region.csv



## pfizer vaccine

  models_in70s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s noncoviddeath pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_noncoviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_in70s_noncoviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_noncoviddeath_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


  report_in70s_noncoviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s noncoviddeath az all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_in70s]
    outputs:
      highly_sensitive:
        models: output/in70s/coviddeath/any/all/*/model*.rds
        data: output/in70s/coviddeath/any/all/*/data*.rds
        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: [data_define_cohorts, models_in70s_coviddeath_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


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


  # models_cox_in70s_coviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s coviddeath any all region
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/coviddeath/any/all/*/region/modelcox*.rds
  #
  # report_cox_in70s_coviddeath_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s coviddeath any all region
  #   needs: [data_define_cohorts, models_cox_in70s_coviddeath_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/coviddeath/any/all/*cox_region.svg
  #       tables: output/in70s/coviddeath/any/all/*cox_region.csv


## pfizer vaccine

  models_in70s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s coviddeath pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_coviddeath_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


  report_in70s_coviddeath_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_coviddeath_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


  report_in70s_coviddeath_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s coviddeath az all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_death_any_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


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


  # models_cox_in70s_death_any_all_region:
  #   run: r:latest analysis/R/dose_1/model_cox.R in70s death any all region
  #   needs: [data_define_cohorts, data_stset_in70s]
  #   outputs:
  #     highly_sensitive:
  #       models: output/in70s/death/any/all/*/region/modelcox*.rds
  #
  # report_cox_in70s_death_any_all_region:
  #   run: r:latest analysis/R/dose_1/report_cox.R in70s death any all region
  #   needs: [data_define_cohorts, models_cox_in70s_death_any_all_region]
  #   outputs:
  #     moderately_sensitive:
  #       plots: output/in70s/death/any/all/*cox_region.svg
  #       tables: output/in70s/death/any/all/*cox_region.csv


## pfizer vaccine

  models_in70s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/model_msm.R in70s death pfizer all
    needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_death_pfizer_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv

  report_in70s_death_pfizer_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s death pfizer all
    needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_in70s_death_az_all]
    outputs:
      highly_sensitive:
        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/*/tab*.csv


  report_in70s_death_az_all:
    run: r:latest analysis/R/dose_1/report_msm.R in70s death az all
    needs: [data_define_cohorts, 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: [data_define_cohorts, 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: [data_define_cohorts, 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: [data_define_cohorts, 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_in70s_all:
    run: r:latest analysis/R/dose_1/report_alloutcomes_combined.R in70s all
    needs: [data_define_cohorts, 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
        tables: output/in70s/*_all.csv




  report_ipw_in70s_any_all:
    run: r:latest analysis/R/dose_1/report_allipw.R in70s any all
    needs: [data_define_cohorts, report_ipw_in70s_postest_any_all, report_ipw_in70s_covidadmitted_any_all, report_ipw_in70s_coviddeath_any_all, report_ipw_in70s_noncoviddeath_any_all, report_ipw_in70s_death_any_all]
    outputs:
      moderately_sensitive:
        svg: output/in70s/plot_vaxany1.svg
        html: output/in70s/tab_vaxany1.html

  report_ipw_in70s_pfizer_all:
    run: r:latest analysis/R/dose_1/report_allipw.R in70s pfizer all
    needs: [data_define_cohorts, report_ipw_in70s_postest_pfizer_all, report_ipw_in70s_covidadmitted_pfizer_all, report_ipw_in70s_coviddeath_pfizer_all, report_ipw_in70s_noncoviddeath_pfizer_all, report_ipw_in70s_death_pfizer_all]
    outputs:
      moderately_sensitive:
        svg: output/in70s/plot_vaxpfizer1.svg
        html: output/in70s/tab_vaxpfizer1.html

  report_ipw_in70s_az_all:
    run: r:latest analysis/R/dose_1/report_allipw.R in70s az all
    needs: [data_define_cohorts, report_ipw_in70s_postest_az_all, report_ipw_in70s_covidadmitted_az_all, report_ipw_in70s_coviddeath_az_all, report_ipw_in70s_noncoviddeath_az_all, report_ipw_in70s_death_az_all]
    outputs:
      moderately_sensitive:
        svg: output/in70s/plot_vaxaz1.svg
        html: output/in70s/tab_vaxaz1.html


  report_ipw_in70s_all:
    run: r:latest analysis/R/dose_1/report_vaxmodel.R in70s all
    needs: [data_define_cohorts, 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