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/
project.yaml
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/
project.yaml
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version: "3.0"
expectations:
population_size: 100000
actions:
generate_cohort:
run: cohortextractor:latest generate_cohort
outputs:
highly_sensitive:
cohort1: output/input_af.csv
cohort2: output/input_af_population_flow_chart.csv
cohort3: output/input_general_population.csv
cohort4: output/input_general_population_flow_chart.csv
# Flowchart for AF population
flowchart_af:
run: stata-mp:latest analysis/flow_chart_af_population.do af_population_flowchart
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: output/oac_log/flow_chart_af_population.log
# Flowchart for general population (before matching)
flowchart_general_population:
run: stata-mp:latest analysis/flow_chart_general_population.do general_population_flowchart
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: output/oac_log/flow_chart_general_population.log
# Main Analysis 1
# Objective 1: compare AF treated people with AF non-treated people
format_dataset_af_oac:
run: stata-mp:latest analysis/00_cr_create_analysis_dataset.do af_oac input_af
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: output/oac_log/00_cr_create_analysis_dataset.log
highly_sensitive:
data: "output/oac_tempdata/format_dataset.dta"
create_dataset_af_oac:
run: stata-mp:latest analysis/01_cr_create_exposure_outcome_af.do af_oac
needs: [format_dataset_af_oac]
outputs:
moderately_sensitive:
log: output/oac_log/01_cr_create_exposure_outcome_af.log
highly_sensitive:
data: "output/oac_tempdata/cr_dataset_af.dta"
# Export case dataset for matching
02ai_exportfile_matching:
run: stata-mp:latest analysis/02ai_exportfile_matching.do af_oac
needs: [create_dataset_af_oac]
outputs:
moderately_sensitive:
log: output/oac_log/02ai_exportfile_matching.log
highly_sensitive:
data1: "output/input_af_oac.csv"
data2: "output/input_af_oac.dta"
# Primary Outcomes: ONS COVID-19 death
02aii_cr_create_population_af_oac_onscoviddeath:
run: stata-mp:latest analysis/02aii_cr_create_population.do onscoviddeath af_oac
needs: [create_dataset_af_oac]
outputs:
moderately_sensitive:
log: output/oac_log/02aii_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/oac_tempdata/analysis_dataset_onscoviddeath.dta"
data2: "output/oac_tempdata/analysis_dataset_STSET_onscoviddeath.dta"
03_an_checks_af_oac_onscoviddeath:
run: stata-mp:latest analysis/03_an_checks.do onscoviddeath af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/03_an_checks_onscoviddeath.log
04_an_descriptive_table_af_oac_onscoviddeath:
run: stata-mp:latest analysis/04_an_descriptive_table.do onscoviddeath af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/04_an_descriptive_table_onscoviddeath.log
table: "output/oac_tabfig/table1_onscoviddeath.txt"
05a_an_models_af_oac_onscoviddeath:
run: stata-mp:latest analysis/05a_an_models.do onscoviddeath af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/05a_an_models_onscoviddeath.log
table: "output/oac_tabfig/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_tempdata/onscoviddeath_univar.ster"
data2: "output/oac_tempdata/onscoviddeath_multivar1.ster"
data3: "output/oac_tempdata/onscoviddeath_multivar2.ster"
data4: "output/oac_tempdata/onscoviddeath_multivar3.ster"
06a_an_models_ethnicity_af_oac_onscoviddeath:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do onscoviddeath af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/06a_an_models_ethnicity_onscoviddeath.log
table: "output/oac_tabfig/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_tempdata/onscoviddeath_univar_ethn.ster"
data2: "output/oac_tempdata/onscoviddeath_multivar1_ethn.ster"
data3: "output/oac_tempdata/onscoviddeath_multivar2_ethn.ster"
data4: "output/oac_tempdata/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/onscoviddeath_multivar3_ethn.ster"
data6: "output/oac_tempdata/onscoviddeath_multivar3_withoutethn.ster"
07_an_model_explore_af_oac_onscoviddeath:
run: stata-mp:latest analysis/07_an_model_explore.do onscoviddeath af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/07_an_model_explore_onscoviddeath.log
table: "output/oac_tabfig/table4_onscoviddeath.txt"
08a_an_model_checks_af_oac_onscoviddeath:
run: stata-mp:latest analysis/08a_an_model_checks.do onscoviddeath af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/08a_an_model_checks_onscoviddeath.log
fig1: "output/oac_tabfig/onscoviddeath_schoenplot1.svg"
fig2: "output/oac_tabfig/onscoviddeath_schoenplot2.svg"
fig3: "output/oac_tabfig/onscoviddeath_schoenplot3.svg"
fig4: "output/oac_tabfig/onscoviddeath_schoenplot4.svg"
table1: "output/oac_tabfig/table5_onscoviddeath.txt"
fig5: "output/oac_tabfig/onscoviddeath_schoenplot1_completecase.svg"
fig6: "output/oac_tabfig/onscoviddeath_schoenplot2_completecase.svg"
fig7: "output/oac_tabfig/onscoviddeath_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_tabfig/onscoviddeath_schoenplot3_completecase.svg"
fig9: "output/oac_tabfig/onscoviddeath_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_tabfig/onscoviddeath_schoenplot4_completecase.svg"
table2: "output/oac_tabfig/table6_onscoviddeath.txt"
09a_an_models_plot_af_oac_onscoviddeath:
run: stata-mp:latest analysis/09a_an_models_plot.do onscoviddeath af_oac 3 0.5 0.1
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/09a_an_models_plot_onscoviddeath.log
fig1: "output/oac_tabfig/adj_curves_onscoviddeath.svg"
fig2: "output/oac_tabfig/diff_curves_onscoviddeath.svg"
# Primary Outcomes: COVID-19 hospital admission
02aii_cr_create_population_af_oac_admitcovid:
run: stata-mp:latest analysis/02aii_cr_create_population.do admitcovid af_oac
needs: [create_dataset_af_oac]
outputs:
moderately_sensitive:
log: output/oac_log/02aii_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/oac_tempdata/analysis_dataset_admitcovid.dta"
data2: "output/oac_tempdata/analysis_dataset_STSET_admitcovid.dta"
03_an_checks_af_oac_admitcovid:
run: stata-mp:latest analysis/03_an_checks.do admitcovid af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/03_an_checks_admitcovid.log
04_an_descriptive_table_af_oac_admitcovid:
run: stata-mp:latest analysis/04_an_descriptive_table.do admitcovid af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/04_an_descriptive_table_admitcovid.log
table: "output/oac_tabfig/table1_admitcovid.txt"
05a_an_models_af_oac_admitcovid:
run: stata-mp:latest analysis/05a_an_models.do admitcovid af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/05a_an_models_admitcovid.log
table: "output/oac_tabfig/table2_admitcovid.txt"
highly_sensitive:
data1: "output/oac_tempdata/admitcovid_univar.ster"
data2: "output/oac_tempdata/admitcovid_multivar1.ster"
data3: "output/oac_tempdata/admitcovid_multivar2.ster"
data4: "output/oac_tempdata/admitcovid_multivar3.ster"
06a_an_models_ethnicity_af_oac_admitcovid:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do admitcovid af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/06a_an_models_ethnicity_admitcovid.log
table: "output/oac_tabfig/table3_admitcovid.txt"
highly_sensitive:
data1: "output/oac_tempdata/admitcovid_univar_ethn.ster"
data2: "output/oac_tempdata/admitcovid_multivar1_ethn.ster"
data3: "output/oac_tempdata/admitcovid_multivar2_ethn.ster"
data4: "output/oac_tempdata/admitcovid_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/admitcovid_multivar3_ethn.ster"
data6: "output/oac_tempdata/admitcovid_multivar3_withoutethn.ster"
07_an_model_explore_af_oac_admitcovid:
run: stata-mp:latest analysis/07_an_model_explore.do admitcovid af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/07_an_model_explore_admitcovid.log
table: "output/oac_tabfig/table4_admitcovid.txt"
08a_an_model_checks_af_oac_admitcovid:
run: stata-mp:latest analysis/08a_an_model_checks.do admitcovid af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/08a_an_model_checks_admitcovid.log
fig1: "output/oac_tabfig/admitcovid_schoenplot1.svg"
fig2: "output/oac_tabfig/admitcovid_schoenplot2.svg"
fig3: "output/oac_tabfig/admitcovid_schoenplot3.svg"
fig4: "output/oac_tabfig/admitcovid_schoenplot4.svg"
table1: "output/oac_tabfig/table5_admitcovid.txt"
fig5: "output/oac_tabfig/admitcovid_schoenplot1_completecase.svg"
fig6: "output/oac_tabfig/admitcovid_schoenplot2_completecase.svg"
fig7: "output/oac_tabfig/admitcovid_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_tabfig/admitcovid_schoenplot3_completecase.svg"
fig9: "output/oac_tabfig/admitcovid_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_tabfig/admitcovid_schoenplot4_completecase.svg"
table2: "output/oac_tabfig/table6_admitcovid.txt"
09a_an_models_plot_af_oac_admitcovid:
run: stata-mp:latest analysis/09a_an_models_plot.do admitcovid af_oac 2 0.5 0.1
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/09a_an_models_plot_admitcovid.log
fig1: "output/oac_tabfig/adj_curves_admitcovid.svg"
fig2: "output/oac_tabfig/diff_curves_admitcovid.svg"
# Exploratory Outcomes: COVID-19 test
02aii_cr_create_population_af_oac_covidtest:
run: stata-mp:latest analysis/02aii_cr_create_population.do covidtest af_oac
needs: [create_dataset_af_oac]
outputs:
moderately_sensitive:
log: output/oac_log/02aii_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/oac_tempdata/analysis_dataset_covidtest.dta"
data2: "output/oac_tempdata/analysis_dataset_STSET_covidtest.dta"
03_an_checks_af_oac_covidtest:
run: stata-mp:latest analysis/03_an_checks.do covidtest af_oac
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/03_an_checks_covidtest.log
04_an_descriptive_table_af_oac_covidtest:
run: stata-mp:latest analysis/04_an_descriptive_table.do covidtest af_oac
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/04_an_descriptive_table_covidtest.log
table: "output/oac_tabfig/table1_covidtest.txt"
05a_an_models_af_oac_covidtest:
run: stata-mp:latest analysis/05a_an_models.do covidtest af_oac
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/05a_an_models_covidtest.log
table: "output/oac_tabfig/table2_covidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/covidtest_univar.ster"
data2: "output/oac_tempdata/covidtest_multivar1.ster"
data3: "output/oac_tempdata/covidtest_multivar2.ster"
data4: "output/oac_tempdata/covidtest_multivar3.ster"
06a_an_models_ethnicity_af_oac_covidtest:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do covidtest af_oac
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/06a_an_models_ethnicity_covidtest.log
table: "output/oac_tabfig/table3_covidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/covidtest_univar_ethn.ster"
data2: "output/oac_tempdata/covidtest_multivar1_ethn.ster"
data3: "output/oac_tempdata/covidtest_multivar2_ethn.ster"
data4: "output/oac_tempdata/covidtest_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/covidtest_multivar3_ethn.ster"
data6: "output/oac_tempdata/covidtest_multivar3_withoutethn.ster"
08a_an_model_checks_af_oac_covidtest:
run: stata-mp:latest analysis/08a_an_model_checks.do covidtest af_oac
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/08a_an_model_checks_covidtest.log
fig1: "output/oac_tabfig/covidtest_schoenplot1.svg"
fig2: "output/oac_tabfig/covidtest_schoenplot2.svg"
fig3: "output/oac_tabfig/covidtest_schoenplot3.svg"
fig4: "output/oac_tabfig/covidtest_schoenplot4.svg"
table1: "output/oac_tabfig/table5_covidtest.txt"
fig5: "output/oac_tabfig/covidtest_schoenplot1_completecase.svg"
fig6: "output/oac_tabfig/covidtest_schoenplot2_completecase.svg"
fig7: "output/oac_tabfig/covidtest_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_tabfig/covidtest_schoenplot3_completecase.svg"
fig9: "output/oac_tabfig/covidtest_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_tabfig/covidtest_schoenplot4_completecase.svg"
table2: "output/oac_tabfig/table6_covidtest.txt"
09a_an_models_plot_af_oac_covidtest:
run: stata-mp:latest analysis/09a_an_models_plot.do covidtest af_oac 3 7 1
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/09a_an_models_plot_covidtest.log
fig1: "output/oac_tabfig/adj_curves_covidtest.svg"
fig2: "output/oac_tabfig/diff_curves_covidtest.svg"
# Exploratory Outcomes: Positive COVID test
02aii_cr_create_population_af_oac_positivecovidtest:
run: stata-mp:latest analysis/02aii_cr_create_population.do positivecovidtest af_oac
needs: [create_dataset_af_oac]
outputs:
moderately_sensitive:
log: output/oac_log/02aii_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/oac_tempdata/analysis_dataset_positivecovidtest.dta"
data2: "output/oac_tempdata/analysis_dataset_STSET_positivecovidtest.dta"
03_an_checks_af_oac_positivecovidtest:
run: stata-mp:latest analysis/03_an_checks.do positivecovidtest af_oac
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/03_an_checks_positivecovidtest.log
04_an_descriptive_table_af_oac_positivecovidtest:
run: stata-mp:latest analysis/04_an_descriptive_table.do positivecovidtest af_oac
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/04_an_descriptive_table_positivecovidtest.log
table: "output/oac_tabfig/table1_positivecovidtest.txt"
05a_an_models_af_oac_positivecovidtest:
run: stata-mp:latest analysis/05a_an_models.do positivecovidtest af_oac
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/05a_an_models_positivecovidtest.log
table: "output/oac_tabfig/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/positivecovidtest_univar.ster"
data2: "output/oac_tempdata/positivecovidtest_multivar1.ster"
data3: "output/oac_tempdata/positivecovidtest_multivar2.ster"
data4: "output/oac_tempdata/positivecovidtest_multivar3.ster"
06a_an_models_ethnicity_af_oac_positivecovidtest:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do positivecovidtest af_oac
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/06a_an_models_ethnicity_positivecovidtest.log
table: "output/oac_tabfig/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/positivecovidtest_univar_ethn.ster"
data2: "output/oac_tempdata/positivecovidtest_multivar1_ethn.ster"
data3: "output/oac_tempdata/positivecovidtest_multivar2_ethn.ster"
data4: "output/oac_tempdata/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/positivecovidtest_multivar3_ethn.ster"
data6: "output/oac_tempdata/positivecovidtest_multivar3_withoutethn.ster"
08a_an_model_checks_af_oac_positivecovidtest:
run: stata-mp:latest analysis/08a_an_model_checks.do positivecovidtest af_oac
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/08a_an_model_checks_positivecovidtest.log
fig1: "output/oac_tabfig/positivecovidtest_schoenplot1.svg"
fig2: "output/oac_tabfig/positivecovidtest_schoenplot2.svg"
fig3: "output/oac_tabfig/positivecovidtest_schoenplot3.svg"
fig4: "output/oac_tabfig/positivecovidtest_schoenplot4.svg"
table1: "output/oac_tabfig/table5_positivecovidtest.txt"
fig5: "output/oac_tabfig/positivecovidtest_schoenplot1_completecase.svg"
fig6: "output/oac_tabfig/positivecovidtest_schoenplot2_completecase.svg"
fig7: "output/oac_tabfig/positivecovidtest_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_tabfig/positivecovidtest_schoenplot3_completecase.svg"
fig9: "output/oac_tabfig/positivecovidtest_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_tabfig/positivecovidtest_schoenplot4_completecase.svg"
table2: "output/oac_tabfig/table6_positivecovidtest.txt"
09a_an_models_plot_af_oac_positivecovidtest:
run: stata-mp:latest analysis/09a_an_models_plot.do positivecovidtest af_oac 3 2 0.5
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/09a_an_models_plot_positivecovidtest.log
fig1: "output/oac_tabfig/adj_curves_positivecovidtest.svg"
fig2: "output/oac_tabfig/diff_curves_positivecovidtest.svg"
# Main Analysis 2
# Objective 2: Compare warfarin users and DOAC users
format_dataset_af_warfarin:
run: stata-mp:latest analysis/00_cr_create_analysis_dataset.do af_warfarin input_af
needs: [generate_cohort]
outputs:
moderately_sensitive:
log: output/warfarin_log/00_cr_create_analysis_dataset.log
highly_sensitive:
data: "output/warfarin_tempdata/format_dataset.dta"
create_dataset_af_warfarin:
run: stata-mp:latest analysis/01_cr_create_exposure_outcome_af.do af_warfarin
needs: [format_dataset_af_warfarin]
outputs:
moderately_sensitive:
log: output/warfarin_log/01_cr_create_exposure_outcome_af.log
highly_sensitive:
data: "output/warfarin_tempdata/cr_dataset_af.dta"
# Primary Outcomes: ONS COVID-19 death
02b_cr_create_population_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/02b_cr_create_population.do onscoviddeath af_warfarin
needs: [create_dataset_af_warfarin]
outputs:
moderately_sensitive:
log: output/warfarin_log/02b_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/analysis_dataset_onscoviddeath.dta"
data2: "output/warfarin_tempdata/analysis_dataset_STSET_onscoviddeath.dta"
03_an_checks_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/03_an_checks.do onscoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/03_an_checks_onscoviddeath.log
04_an_descriptive_table_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/04_an_descriptive_table.do onscoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/04_an_descriptive_table_onscoviddeath.log
table: "output/warfarin_tabfig/table1_onscoviddeath.txt"
05b_an_models_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onscoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/05b_an_models_onscoviddeath.log
table: "output/warfarin_tabfig/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/onscoviddeath_univar.ster"
data2: "output/warfarin_tempdata/onscoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/onscoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/onscoviddeath_multivar3.ster"
06b_an_models_ethnicity_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/06b_an_models_ethnicity_onscoviddeath.log
table: "output/warfarin_tabfig/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/onscoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/onscoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/onscoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/onscoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/onscoviddeath_multivar3_withoutethn.ster"
07_an_model_explore_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/07_an_model_explore.do onscoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/07_an_model_explore_onscoviddeath.log
table: "output/warfarin_tabfig/table4_onscoviddeath.txt"
08b_an_model_checks_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/08b_an_model_checks.do onscoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/08b_an_model_checks_onscoviddeath.log
fig1: "output/warfarin_tabfig/onscoviddeath_schoenplot1.svg"
fig2: "output/warfarin_tabfig/onscoviddeath_schoenplot2.svg"
fig3: "output/warfarin_tabfig/onscoviddeath_schoenplot3.svg"
fig4: "output/warfarin_tabfig/onscoviddeath_schoenplot4.svg"
table1: "output/warfarin_tabfig/table5_onscoviddeath.txt"
fig5: "output/warfarin_tabfig/onscoviddeath_schoenplot1_completecase.svg"
fig6: "output/warfarin_tabfig/onscoviddeath_schoenplot2_completecase.svg"
fig7: "output/warfarin_tabfig/onscoviddeath_schoenplot3_completecase_ethn.svg"
fig8: "output/warfarin_tabfig/onscoviddeath_schoenplot3_completecase.svg"
fig9: "output/warfarin_tabfig/onscoviddeath_schoenplot4_completecase_ethn.svg"
fig10: "output/warfarin_tabfig/onscoviddeath_schoenplot4_completecase.svg"
table2: "output/warfarin_tabfig/table6_onscoviddeath.txt"
09b_an_models_plot_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/09b_an_models_plot.do onscoviddeath af_warfarin 2 1 0.1
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/09b_an_models_plot_onscoviddeath.log
fig1: "output/warfarin_tabfig/adj_curves_onscoviddeath.svg"
fig2: "output/warfarin_tabfig/diff_curves_onscoviddeath.svg"
# Primary Outcomes: COVID-19 hospital admission
02b_cr_create_population_af_warfarin_admitcovid:
run: stata-mp:latest analysis/02b_cr_create_population.do admitcovid af_warfarin
needs: [create_dataset_af_warfarin]
outputs:
moderately_sensitive:
log: output/warfarin_log/02b_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/warfarin_tempdata/analysis_dataset_admitcovid.dta"
data2: "output/warfarin_tempdata/analysis_dataset_STSET_admitcovid.dta"
03_an_checks_af_warfarin_admitcovid:
run: stata-mp:latest analysis/03_an_checks.do admitcovid af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/03_an_checks_admitcovid.log
04_an_descriptive_table_af_warfarin_admitcovid:
run: stata-mp:latest analysis/04_an_descriptive_table.do admitcovid af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/04_an_descriptive_table_admitcovid.log
table: "output/warfarin_tabfig/table1_admitcovid.txt"
05b_an_models_af_warfarin_admitcovid:
run: stata-mp:latest analysis/05b_an_models.do admitcovid af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/05b_an_models_admitcovid.log
table: "output/warfarin_tabfig/table2_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/admitcovid_univar.ster"
data2: "output/warfarin_tempdata/admitcovid_multivar1.ster"
data3: "output/warfarin_tempdata/admitcovid_multivar2.ster"
data4: "output/warfarin_tempdata/admitcovid_multivar3.ster"
06b_an_models_ethnicity_af_warfarin_admitcovid:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/06b_an_models_ethnicity_admitcovid.log
table: "output/warfarin_tabfig/table3_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/admitcovid_univar_ethn.ster"
data2: "output/warfarin_tempdata/admitcovid_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/admitcovid_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/admitcovid_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/admitcovid_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/admitcovid_multivar3_withoutethn.ster"
07_an_model_explore_af_warfarin_admitcovid:
run: stata-mp:latest analysis/07_an_model_explore.do admitcovid af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/07_an_model_explore_admitcovid.log
table: "output/warfarin_tabfig/table4_admitcovid.txt"
08b_an_model_checks_af_warfarin_admitcovid:
run: stata-mp:latest analysis/08b_an_model_checks.do admitcovid af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/08b_an_model_checks_admitcovid.log
fig1: "output/warfarin_tabfig/admitcovid_schoenplot1.svg"
fig2: "output/warfarin_tabfig/admitcovid_schoenplot2.svg"
fig3: "output/warfarin_tabfig/admitcovid_schoenplot3.svg"
fig4: "output/warfarin_tabfig/admitcovid_schoenplot4.svg"
table1: "output/warfarin_tabfig/table5_admitcovid.txt"
fig5: "output/warfarin_tabfig/admitcovid_schoenplot1_completecase.svg"
fig6: "output/warfarin_tabfig/admitcovid_schoenplot2_completecase.svg"
fig7: "output/warfarin_tabfig/admitcovid_schoenplot3_completecase_ethn.svg"
fig8: "output/warfarin_tabfig/admitcovid_schoenplot3_completecase.svg"
fig9: "output/warfarin_tabfig/admitcovid_schoenplot4_completecase_ethn.svg"
fig10: "output/warfarin_tabfig/admitcovid_schoenplot4_completecase.svg"
table2: "output/warfarin_tabfig/table6_admitcovid.txt"
09b_an_models_plot_af_warfarin_admitcovid:
run: stata-mp:latest analysis/09b_an_models_plot.do admitcovid af_warfarin 2 1 0.1
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/09b_an_models_plot_admitcovid.log
fig1: "output/warfarin_tabfig/adj_curves_admitcovid.svg"
fig2: "output/warfarin_tabfig/diff_curves_admitcovid.svg"
# Exploratory Outcomes: Non-COVID death
02b_cr_create_population_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/02b_cr_create_population.do onsnoncoviddeath af_warfarin
needs: [create_dataset_af_warfarin]
outputs:
moderately_sensitive:
log: output/warfarin_log/02b_cr_create_population_onsnoncoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/analysis_dataset_onsnoncoviddeath.dta"
data2: "output/warfarin_tempdata/analysis_dataset_STSET_onsnoncoviddeath.dta"
03_an_checks_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/03_an_checks.do onsnoncoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/03_an_checks_onsnoncoviddeath.log
04_an_descriptive_table_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/04_an_descriptive_table.do onsnoncoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/04_an_descriptive_table_onsnoncoviddeath.log
table: "output/warfarin_tabfig/table1_onsnoncoviddeath.txt"
05b_an_models_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/05b_an_models_onsnoncoviddeath.log
table: "output/warfarin_tabfig/table2_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/onsnoncoviddeath_univar.ster"
data2: "output/warfarin_tempdata/onsnoncoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/onsnoncoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/onsnoncoviddeath_multivar3.ster"
06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/06b_an_models_ethnicity_onsnoncoviddeath.log
table: "output/warfarin_tabfig/table3_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/onsnoncoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/onsnoncoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/onsnoncoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/onsnoncoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/onsnoncoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/onsnoncoviddeath_multivar3_withoutethn.ster"
08b_an_model_checks_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/08b_an_model_checks.do onsnoncoviddeath af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/08b_an_model_checks_onsnoncoviddeath.log
fig1: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot1.svg"
fig2: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot2.svg"
fig3: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot3.svg"
fig4: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot4.svg"
table1: "output/warfarin_tabfig/table5_onsnoncoviddeath.txt"
fig5: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot1_completecase.svg"
fig6: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot2_completecase.svg"
fig7: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot3_completecase_ethn.svg"
fig8: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot3_completecase.svg"
fig9: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot4_completecase_ethn.svg"
fig10: "output/warfarin_tabfig/onsnoncoviddeath_schoenplot4_completecase.svg"
table2: "output/warfarin_tabfig/table6_onsnoncoviddeath.txt"
09b_an_models_plot_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/09b_an_models_plot.do onsnoncoviddeath af_warfarin 3 5 1
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/09b_an_models_plot_onsnoncoviddeath.log
fig1: "output/warfarin_tabfig/adj_curves_onsnoncoviddeath.svg"
fig2: "output/warfarin_tabfig/diff_curves_onsnoncoviddeath.svg"
# Exploratory Outcomes: COVID-19 test
02b_cr_create_population_af_warfarin_covidtest:
run: stata-mp:latest analysis/02b_cr_create_population.do covidtest af_warfarin
needs: [create_dataset_af_warfarin]
outputs:
moderately_sensitive:
log: output/warfarin_log/02b_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/analysis_dataset_covidtest.dta"
data2: "output/warfarin_tempdata/analysis_dataset_STSET_covidtest.dta"
03_an_checks_af_warfarin_covidtest:
run: stata-mp:latest analysis/03_an_checks.do covidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/03_an_checks_covidtest.log
04_an_descriptive_table_af_warfarin_covidtest:
run: stata-mp:latest analysis/04_an_descriptive_table.do covidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/04_an_descriptive_table_covidtest.log
table: "output/warfarin_tabfig/table1_covidtest.txt"
05b_an_models_af_warfarin_covidtest:
run: stata-mp:latest analysis/05b_an_models.do covidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/05b_an_models_covidtest.log
table: "output/warfarin_tabfig/table2_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/covidtest_univar.ster"
data2: "output/warfarin_tempdata/covidtest_multivar1.ster"
data3: "output/warfarin_tempdata/covidtest_multivar2.ster"
data4: "output/warfarin_tempdata/covidtest_multivar3.ster"
06b_an_models_ethnicity_af_warfarin_covidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/06b_an_models_ethnicity_covidtest.log
table: "output/warfarin_tabfig/table3_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/covidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/covidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/covidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/covidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/covidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/covidtest_multivar3_withoutethn.ster"
08b_an_model_checks_af_warfarin_covidtest:
run: stata-mp:latest analysis/08b_an_model_checks.do covidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/08b_an_model_checks_covidtest.log
fig1: "output/warfarin_tabfig/covidtest_schoenplot1.svg"
fig2: "output/warfarin_tabfig/covidtest_schoenplot2.svg"
fig3: "output/warfarin_tabfig/covidtest_schoenplot3.svg"
fig4: "output/warfarin_tabfig/covidtest_schoenplot4.svg"
table1: "output/warfarin_tabfig/table5_covidtest.txt"
fig5: "output/warfarin_tabfig/covidtest_schoenplot1_completecase.svg"
fig6: "output/warfarin_tabfig/covidtest_schoenplot2_completecase.svg"
fig7: "output/warfarin_tabfig/covidtest_schoenplot3_completecase_ethn.svg"
fig8: "output/warfarin_tabfig/covidtest_schoenplot3_completecase.svg"
fig9: "output/warfarin_tabfig/covidtest_schoenplot4_completecase_ethn.svg"
fig10: "output/warfarin_tabfig/covidtest_schoenplot4_completecase.svg"
table2: "output/warfarin_tabfig/table6_covidtest.txt"
09b_an_models_plot_af_warfarin_covidtest:
run: stata-mp:latest analysis/09b_an_models_plot.do covidtest af_warfarin 3 10 1
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/09b_an_models_plot_covidtest.log
fig1: "output/warfarin_tabfig/adj_curves_covidtest.svg"
fig2: "output/warfarin_tabfig/diff_curves_covidtest.svg"
# Exploratory Outcomes: Positive COVID test
02b_cr_create_population_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/02b_cr_create_population.do positivecovidtest af_warfarin
needs: [create_dataset_af_warfarin]
outputs:
moderately_sensitive:
log: output/warfarin_log/02b_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/analysis_dataset_positivecovidtest.dta"
data2: "output/warfarin_tempdata/analysis_dataset_STSET_positivecovidtest.dta"
03_an_checks_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/03_an_checks.do positivecovidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/03_an_checks_positivecovidtest.log
04_an_descriptive_table_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/04_an_descriptive_table.do positivecovidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/04_an_descriptive_table_positivecovidtest.log
table: "output/warfarin_tabfig/table1_positivecovidtest.txt"
05b_an_models_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/05b_an_models.do positivecovidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/05b_an_models_positivecovidtest.log
table: "output/warfarin_tabfig/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/positivecovidtest_univar.ster"
data2: "output/warfarin_tempdata/positivecovidtest_multivar1.ster"
data3: "output/warfarin_tempdata/positivecovidtest_multivar2.ster"
data4: "output/warfarin_tempdata/positivecovidtest_multivar3.ster"
06b_an_models_ethnicity_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/06b_an_models_ethnicity_positivecovidtest.log
table: "output/warfarin_tabfig/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/positivecovidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/positivecovidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/positivecovidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/positivecovidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/positivecovidtest_multivar3_withoutethn.ster"
08b_an_model_checks_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/08b_an_model_checks.do positivecovidtest af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/08b_an_model_checks_positivecovidtest.log
fig1: "output/warfarin_tabfig/positivecovidtest_schoenplot1.svg"
fig2: "output/warfarin_tabfig/positivecovidtest_schoenplot2.svg"
fig3: "output/warfarin_tabfig/positivecovidtest_schoenplot3.svg"
fig4: "output/warfarin_tabfig/positivecovidtest_schoenplot4.svg"
table1: "output/warfarin_tabfig/table5_positivecovidtest.txt"
fig5: "output/warfarin_tabfig/positivecovidtest_schoenplot1_completecase.svg"
fig6: "output/warfarin_tabfig/positivecovidtest_schoenplot2_completecase.svg"
fig7: "output/warfarin_tabfig/positivecovidtest_schoenplot3_completecase_ethn.svg"
fig8: "output/warfarin_tabfig/positivecovidtest_schoenplot3_completecase.svg"
fig9: "output/warfarin_tabfig/positivecovidtest_schoenplot4_completecase_ethn.svg"
fig10: "output/warfarin_tabfig/positivecovidtest_schoenplot4_completecase.svg"
table2: "output/warfarin_tabfig/table6_positivecovidtest.txt"
09b_an_models_plot_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/09b_an_models_plot.do positivecovidtest af_warfarin 2 1.5 0.1
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/09b_an_models_plot_positivecovidtest.log
fig1: "output/warfarin_tabfig/adj_curves_positivecovidtest.svg"
fig2: "output/warfarin_tabfig/diff_curves_positivecovidtest.svg"
# Main Analysis 3
# Objective 1: compare AF treated people with general population
matching:
run: python:latest python analysis/match_running.py
needs: [generate_cohort, 02ai_exportfile_matching]
outputs:
moderately_sensitive:
log: output/matching_report_af_gen_pop.txt
highly_sensitive:
data1: "output/matched_cases_af_gen_pop.csv"
data2: "output/matched_matches_af_gen_pop.csv"
format_dataset_af_match:
run: stata-mp:latest analysis/00_cr_create_analysis_dataset.do af_match matched_matches_af_gen_pop
needs: [generate_cohort, matching]
outputs:
moderately_sensitive:
log: output/oac_match_log/00_cr_create_analysis_dataset.log
highly_sensitive:
data: "output/oac_match_tempdata/format_dataset.dta"
create_dataset_af_match:
run: stata-mp:latest analysis/01c_cr_create_exposure_outcome_af_match.do af_match
needs: [format_dataset_af_match, matching]
outputs:
moderately_sensitive:
log: output/oac_match_log/01c_cr_create_exposure_outcome_af_match.log
highly_sensitive:
data: "output/oac_match_tempdata/cr_dataset_af.dta"
# Primary Outcomes: ONS COVID-19 death
02c_cr_create_population_af_match_onscoviddeath:
run: stata-mp:latest analysis/02c_cr_create_population.do onscoviddeath af_match matched_cases_af_gen_pop
needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
outputs:
moderately_sensitive:
log: output/oac_match_log/02c_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/oac_match_tempdata/matched_control_onscoviddeath.dta"
data2: "output/oac_match_tempdata/analysis_dataset_onscoviddeath.dta"
data3: "output/oac_match_tempdata/analysis_dataset_STSET_onscoviddeath.dta"
03_an_checks_af_match_onscoviddeath:
run: stata-mp:latest analysis/03_an_checks.do onscoviddeath af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/03_an_checks_onscoviddeath.log
04_an_descriptive_table_af_match_onscoviddeath:
run: stata-mp:latest analysis/04_an_descriptive_table.do onscoviddeath af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/04_an_descriptive_table_onscoviddeath.log
table: "output/oac_match_tabfig/table1_onscoviddeath.txt"
05c_an_models_af_match_onscoviddeath:
run: stata-mp:latest analysis/05c_an_models.do onscoviddeath af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/05c_an_models_onscoviddeath.log
table: "output/oac_match_tabfig/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/onscoviddeath_univar.ster"
data2: "output/oac_match_tempdata/onscoviddeath_multivar1.ster"
data3: "output/oac_match_tempdata/onscoviddeath_multivar2.ster"
data4: "output/oac_match_tempdata/onscoviddeath_multivar3.ster"
06c_an_models_ethnicity_af_match_onscoviddeath:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do onscoviddeath af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/06c_an_models_ethnicity_onscoviddeath.log
table: "output/oac_match_tabfig/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/onscoviddeath_univar_ethn.ster"
data2: "output/oac_match_tempdata/onscoviddeath_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/onscoviddeath_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/onscoviddeath_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/onscoviddeath_multivar3_withoutethn.ster"
07_an_model_explore_af_match_onscoviddeath:
run: stata-mp:latest analysis/07_an_model_explore.do onscoviddeath af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/07_an_model_explore_onscoviddeath.log
table: "output/oac_match_tabfig/table4_onscoviddeath.txt"
08c_an_model_checks_af_match_onscoviddeath:
run: stata-mp:latest analysis/08c_an_model_checks.do onscoviddeath af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/08c_an_model_checks_onscoviddeath.log
fig1: "output/oac_match_tabfig/onscoviddeath_schoenplot1.svg"
fig2: "output/oac_match_tabfig/onscoviddeath_schoenplot2.svg"
fig3: "output/oac_match_tabfig/onscoviddeath_schoenplot3.svg"
fig4: "output/oac_match_tabfig/onscoviddeath_schoenplot4.svg"
table1: "output/oac_match_tabfig/table5_onscoviddeath.txt"
fig5: "output/oac_match_tabfig/onscoviddeath_schoenplot1_completecase.svg"
fig6: "output/oac_match_tabfig/onscoviddeath_schoenplot2_completecase.svg"
fig7: "output/oac_match_tabfig/onscoviddeath_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_match_tabfig/onscoviddeath_schoenplot3_completecase.svg"
fig9: "output/oac_match_tabfig/onscoviddeath_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_match_tabfig/onscoviddeath_schoenplot4_completecase.svg"
table2: "output/oac_match_tabfig/table6_onscoviddeath.txt"
09a_an_models_plot_af_match_onscoviddeath:
run: stata-mp:latest analysis/09a_an_models_plot.do onscoviddeath af_match 1 0.5 0.1
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/09a_an_models_plot_onscoviddeath.log
fig1: "output/oac_match_tabfig/adj_curves_onscoviddeath.svg"
fig2: "output/oac_match_tabfig/diff_curves_onscoviddeath.svg"
# Primary Outcomes: COVID-19 hospital admission
02c_cr_create_population_af_match_admitcovid:
run: stata-mp:latest analysis/02c_cr_create_population.do admitcovid af_match matched_cases_af_gen_pop
needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
outputs:
moderately_sensitive:
log: output/oac_match_log/02c_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/oac_match_tempdata/matched_control_admitcovid.dta"
data2: "output/oac_match_tempdata/analysis_dataset_admitcovid.dta"
data3: "output/oac_match_tempdata/analysis_dataset_STSET_admitcovid.dta"
03_an_checks_af_match_admitcovid:
run: stata-mp:latest analysis/03_an_checks.do admitcovid af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/03_an_checks_admitcovid.log
04_an_descriptive_table_af_match_admitcovid:
run: stata-mp:latest analysis/04_an_descriptive_table.do admitcovid af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/04_an_descriptive_table_admitcovid.log
table: "output/oac_match_tabfig/table1_admitcovid.txt"