Job request: 489
- Organisation:
- The London School of Hygiene & Tropical Medicine
- Workspace:
- anticoagulant-sensitivity-analysis-5-check
- ID:
- yvk5yfmktoeetwab
This page shows the technical details of what happened when authorised researcher Angel Wong requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
moderately_sensitive
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
moderately_sensitive
can be requested for release to the public, via a controlled
output review service.
Jobs
-
- Job identifier:
-
wxwprqvwx6odlhxf
Pipeline
Show project.yaml
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
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
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"
05c_an_models_af_match_admitcovid:
run: stata-mp:latest analysis/05c_an_models.do admitcovid af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/05c_an_models_admitcovid.log
table: "output/oac_match_tabfig/table2_admitcovid.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/admitcovid_univar.ster"
data2: "output/oac_match_tempdata/admitcovid_multivar1.ster"
data3: "output/oac_match_tempdata/admitcovid_multivar2.ster"
data4: "output/oac_match_tempdata/admitcovid_multivar3.ster"
06c_an_models_ethnicity_af_match_admitcovid:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do admitcovid af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/06c_an_models_ethnicity_admitcovid.log
table: "output/oac_match_tabfig/table3_admitcovid.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/admitcovid_univar_ethn.ster"
data2: "output/oac_match_tempdata/admitcovid_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/admitcovid_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/admitcovid_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/admitcovid_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/admitcovid_multivar3_withoutethn.ster"
07_an_model_explore_af_match_admitcovid:
run: stata-mp:latest analysis/07_an_model_explore.do admitcovid af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/07_an_model_explore_admitcovid.log
table: "output/oac_match_tabfig/table4_admitcovid.txt"
08c_an_model_checks_af_match_admitcovid:
run: stata-mp:latest analysis/08c_an_model_checks.do admitcovid af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/08c_an_model_checks_admitcovid.log
fig1: "output/oac_match_tabfig/admitcovid_schoenplot1.svg"
fig2: "output/oac_match_tabfig/admitcovid_schoenplot2.svg"
fig3: "output/oac_match_tabfig/admitcovid_schoenplot3.svg"
fig4: "output/oac_match_tabfig/admitcovid_schoenplot4.svg"
table1: "output/oac_match_tabfig/table5_admitcovid.txt"
fig5: "output/oac_match_tabfig/admitcovid_schoenplot1_completecase.svg"
fig6: "output/oac_match_tabfig/admitcovid_schoenplot2_completecase.svg"
fig7: "output/oac_match_tabfig/admitcovid_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_match_tabfig/admitcovid_schoenplot3_completecase.svg"
fig9: "output/oac_match_tabfig/admitcovid_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_match_tabfig/admitcovid_schoenplot4_completecase.svg"
table2: "output/oac_match_tabfig/table6_admitcovid.txt"
09a_an_models_plot_af_match_admitcovid:
run: stata-mp:latest analysis/09a_an_models_plot.do admitcovid af_match 2 0.5 0.1
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/09a_an_models_plot_admitcovid.log
fig1: "output/oac_match_tabfig/adj_curves_admitcovid.svg"
fig2: "output/oac_match_tabfig/diff_curves_admitcovid.svg"
# Exploratory Outcomes: COVID-19 test
02c_cr_create_population_af_match_covidtest:
run: stata-mp:latest analysis/02c_cr_create_population.do covidtest af_match
needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
outputs:
moderately_sensitive:
log: output/oac_match_log/02c_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/oac_match_tempdata/matched_control_covidtest.dta"
data2: "output/oac_match_tempdata/analysis_dataset_covidtest.dta"
data3: "output/oac_match_tempdata/analysis_dataset_STSET_covidtest.dta"
03_an_checks_af_match_covidtest:
run: stata-mp:latest analysis/03_an_checks.do covidtest af_match
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/03_an_checks_covidtest.log
04_an_descriptive_table_af_match_covidtest:
run: stata-mp:latest analysis/04_an_descriptive_table.do covidtest af_match
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/04_an_descriptive_table_covidtest.log
table: "output/oac_match_tabfig/table1_covidtest.txt"
05c_an_models_af_match_covidtest:
run: stata-mp:latest analysis/05c_an_models.do covidtest af_match
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/05c_an_models_covidtest.log
table: "output/oac_match_tabfig/table2_covidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/covidtest_univar.ster"
data2: "output/oac_match_tempdata/covidtest_multivar1.ster"
data3: "output/oac_match_tempdata/covidtest_multivar2.ster"
data4: "output/oac_match_tempdata/covidtest_multivar3.ster"
06c_an_models_ethnicity_af_match_covidtest:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do covidtest af_match
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/06c_an_models_ethnicity_covidtest.log
table: "output/oac_match_tabfig/table3_covidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/covidtest_univar_ethn.ster"
data2: "output/oac_match_tempdata/covidtest_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/covidtest_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/covidtest_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/covidtest_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/covidtest_multivar3_withoutethn.ster"
08c_an_model_checks_af_match_covidtest:
run: stata-mp:latest analysis/08c_an_model_checks.do covidtest af_match
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/08c_an_model_checks_covidtest.log
fig1: "output/oac_match_tabfig/covidtest_schoenplot1.svg"
fig2: "output/oac_match_tabfig/covidtest_schoenplot2.svg"
fig3: "output/oac_match_tabfig/covidtest_schoenplot3.svg"
fig4: "output/oac_match_tabfig/covidtest_schoenplot4.svg"
table1: "output/oac_match_tabfig/table5_covidtest.txt"
fig5: "output/oac_match_tabfig/covidtest_schoenplot1_completecase.svg"
fig6: "output/oac_match_tabfig/covidtest_schoenplot2_completecase.svg"
fig7: "output/oac_match_tabfig/covidtest_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_match_tabfig/covidtest_schoenplot3_completecase.svg"
fig9: "output/oac_match_tabfig/covidtest_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_match_tabfig/covidtest_schoenplot4_completecase.svg"
table2: "output/oac_match_tabfig/table6_covidtest.txt"
09a_an_models_plot_af_match_covidtest:
run: stata-mp:latest analysis/09a_an_models_plot.do covidtest af_match 3 10 1
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/09a_an_models_plot_covidtest.log
fig1: "output/oac_match_tabfig/adj_curves_covidtest.svg"
fig2: "output/oac_match_tabfig/diff_curves_covidtest.svg"
# Exploratory Outcomes: Positive COVID test
02c_cr_create_population_af_match_positivecovidtest:
run: stata-mp:latest analysis/02c_cr_create_population.do positivecovidtest af_match
needs: [create_dataset_af_match, matching, 02ai_exportfile_matching]
outputs:
moderately_sensitive:
log: output/oac_match_log/02c_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/oac_match_tempdata/matched_control_positivecovidtest.dta"
data2: "output/oac_match_tempdata/analysis_dataset_positivecovidtest.dta"
data3: "output/oac_match_tempdata/analysis_dataset_STSET_positivecovidtest.dta"
03_an_checks_af_match_positivecovidtest:
run: stata-mp:latest analysis/03_an_checks.do positivecovidtest af_match
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/03_an_checks_positivecovidtest.log
04_an_descriptive_table_af_match_positivecovidtest:
run: stata-mp:latest analysis/04_an_descriptive_table.do positivecovidtest af_match
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/04_an_descriptive_table_positivecovidtest.log
table: "output/oac_match_tabfig/table1_positivecovidtest.txt"
05c_an_models_af_match_positivecovidtest:
run: stata-mp:latest analysis/05c_an_models.do positivecovidtest af_match
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/05c_an_models_positivecovidtest.log
table: "output/oac_match_tabfig/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/positivecovidtest_univar.ster"
data2: "output/oac_match_tempdata/positivecovidtest_multivar1.ster"
data3: "output/oac_match_tempdata/positivecovidtest_multivar2.ster"
data4: "output/oac_match_tempdata/positivecovidtest_multivar3.ster"
06c_an_models_ethnicity_af_match_positivecovidtest:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do positivecovidtest af_match
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/06c_an_models_ethnicity_positivecovidtest.log
table: "output/oac_match_tabfig/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/positivecovidtest_univar_ethn.ster"
data2: "output/oac_match_tempdata/positivecovidtest_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/positivecovidtest_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/positivecovidtest_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/positivecovidtest_multivar3_withoutethn.ster"
08c_an_model_checks_af_match_positivecovidtest:
run: stata-mp:latest analysis/08c_an_model_checks.do positivecovidtest af_match
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/08c_an_model_checks_positivecovidtest.log
fig1: "output/oac_match_tabfig/positivecovidtest_schoenplot1.svg"
fig2: "output/oac_match_tabfig/positivecovidtest_schoenplot2.svg"
fig3: "output/oac_match_tabfig/positivecovidtest_schoenplot3.svg"
fig4: "output/oac_match_tabfig/positivecovidtest_schoenplot4.svg"
table1: "output/oac_match_tabfig/table5_positivecovidtest.txt"
fig5: "output/oac_match_tabfig/positivecovidtest_schoenplot1_completecase.svg"
fig6: "output/oac_match_tabfig/positivecovidtest_schoenplot2_completecase.svg"
fig7: "output/oac_match_tabfig/positivecovidtest_schoenplot3_completecase_ethn.svg"
fig8: "output/oac_match_tabfig/positivecovidtest_schoenplot3_completecase.svg"
fig9: "output/oac_match_tabfig/positivecovidtest_schoenplot4_completecase_ethn.svg"
fig10: "output/oac_match_tabfig/positivecovidtest_schoenplot4_completecase.svg"
table2: "output/oac_match_tabfig/table6_positivecovidtest.txt"
09a_an_models_plot_af_match_positivecovidtest:
run: stata-mp:latest analysis/09a_an_models_plot.do positivecovidtest af_match 4 1 0.1
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/09a_an_models_plot_positivecovidtest.log
fig1: "output/oac_match_tabfig/adj_curves_positivecovidtest.svg"
fig2: "output/oac_match_tabfig/diff_curves_positivecovidtest.svg"
# Sensitivity Analysis 1
# Remove people with antiplatelets
# Objective 1: compare AF treated people with AF non-treated people
# Primary Outcomes: ONS COVID-19 death
SA1_02a_cr_create_population_af_oac_onscoviddeath:
run: stata-mp:latest analysis/SA1_02a_cr_create_population.do onscoviddeath SA1_af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_onscoviddeath.dta"
data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_onscoviddeath.dta"
SA1_05a_an_models_af_oac_onscoviddeath:
run: stata-mp:latest analysis/05a_an_models.do onscoviddeath SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_onscoviddeath, 05a_an_models_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/05a_an_models_onscoviddeath.log
table: "output/oac_tabfig/sens_analysis_1/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/onscoviddeath_univar.ster"
data2: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar3.ster"
SA1_06a_an_models_ethnicity_af_oac_onscoviddeath:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do onscoviddeath SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_onscoviddeath, 06a_an_models_ethnicity_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_onscoviddeath.log
table: "output/oac_tabfig/sens_analysis_1/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/onscoviddeath_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_1/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA1_02a_cr_create_population_af_oac_admitcovid:
run: stata-mp:latest analysis/SA1_02a_cr_create_population.do admitcovid SA1_af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_admitcovid.dta"
data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_admitcovid.dta"
SA1_05a_an_models_af_oac_admitcovid:
run: stata-mp:latest analysis/05a_an_models.do admitcovid SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_admitcovid, 05a_an_models_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/05a_an_models_admitcovid.log
table: "output/oac_tabfig/sens_analysis_1/table2_admitcovid.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/admitcovid_univar.ster"
data2: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar3.ster"
SA1_06a_an_models_ethnicity_af_oac_admitcovid:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do admitcovid SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_admitcovid, 06a_an_models_ethnicity_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_admitcovid.log
table: "output/oac_tabfig/sens_analysis_1/table3_admitcovid.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/admitcovid_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_1/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA1_02a_cr_create_population_af_oac_covidtest:
run: stata-mp:latest analysis/SA1_02a_cr_create_population.do covidtest SA1_af_oac
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_covidtest.dta"
data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_covidtest.dta"
SA1_05a_an_models_af_oac_covidtest:
run: stata-mp:latest analysis/05a_an_models.do covidtest SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_covidtest, 05a_an_models_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/05a_an_models_covidtest.log
table: "output/oac_tabfig/sens_analysis_1/table2_covidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/covidtest_univar.ster"
data2: "output/oac_tempdata/sens_analysis_1/covidtest_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_1/covidtest_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_1/covidtest_multivar3.ster"
SA1_06a_an_models_ethnicity_af_oac_covidtest:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do covidtest SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_covidtest, 06a_an_models_ethnicity_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_covidtest.log
table: "output/oac_tabfig/sens_analysis_1/table3_covidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/covidtest_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_1/covidtest_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_1/covidtest_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_1/covidtest_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_1/covidtest_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_1/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA1_02a_cr_create_population_af_oac_positivecovidtest:
run: stata-mp:latest analysis/SA1_02a_cr_create_population.do positivecovidtest SA1_af_oac
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/SA1_02a_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/analysis_dataset_positivecovidtest.dta"
data2: "output/oac_tempdata/sens_analysis_1/analysis_dataset_STSET_positivecovidtest.dta"
SA1_05a_an_models_af_oac_positivecovidtest:
run: stata-mp:latest analysis/05a_an_models.do positivecovidtest SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_positivecovidtest, 05a_an_models_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/05a_an_models_positivecovidtest.log
table: "output/oac_tabfig/sens_analysis_1/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/positivecovidtest_univar.ster"
data2: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar3.ster"
SA1_06a_an_models_ethnicity_af_oac_positivecovidtest:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do positivecovidtest SA1_af_oac
needs: [SA1_02a_cr_create_population_af_oac_positivecovidtest, 06a_an_models_ethnicity_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_1/06a_an_models_ethnicity_positivecovidtest.log
table: "output/oac_tabfig/sens_analysis_1/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_1/positivecovidtest_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_1/positivecovidtest_multivar3_withoutethn.ster"
# Sensitivity Analysis 1
# Remove people with antiplatelets
# Objective 2: Compare warfarin users and DOAC users
# Primary Outcomes: ONS COVID-19 death
SA1_02b_cr_create_population_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/SA1_02b_cr_create_population.do onscoviddeath SA1_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_onscoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_onscoviddeath.dta"
SA1_05b_an_models_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/05b_an_models_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_1/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar3.ster"
SA1_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_1/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_1/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA1_02b_cr_create_population_af_warfarin_admitcovid:
run: stata-mp:latest analysis/SA1_02b_cr_create_population.do admitcovid SA1_af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_admitcovid.dta"
data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_admitcovid.dta"
SA1_05b_an_models_af_warfarin_admitcovid:
run: stata-mp:latest analysis/05b_an_models.do admitcovid SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/05b_an_models_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_1/table2_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/admitcovid_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar3.ster"
SA1_06b_an_models_ethnicity_af_warfarin_admitcovid:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_1/table3_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/admitcovid_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_1/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: Non-COVID death
SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/SA1_02b_cr_create_population.do onsnoncoviddeath SA1_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_onsnoncoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_onsnoncoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_onsnoncoviddeath.dta"
SA1_05b_an_models_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/05b_an_models_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_1/table2_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar3.ster"
SA1_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_1/table3_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_1/onsnoncoviddeath_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA1_02b_cr_create_population_af_warfarin_covidtest:
run: stata-mp:latest analysis/SA1_02b_cr_create_population.do covidtest SA1_af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_covidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_covidtest.dta"
SA1_05b_an_models_af_warfarin_covidtest:
run: stata-mp:latest analysis/05b_an_models.do covidtest SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/05b_an_models_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_1/table2_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/covidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar3.ster"
SA1_06b_an_models_ethnicity_af_warfarin_covidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_1/table3_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/covidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_1/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA1_02b_cr_create_population_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/SA1_02b_cr_create_population.do positivecovidtest SA1_af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/SA1_02b_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_positivecovidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_1/analysis_dataset_STSET_positivecovidtest.dta"
SA1_05b_an_models_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/05b_an_models_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_1/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar3.ster"
SA1_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA1_af_warfarin
needs: [SA1_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_1/06b_an_models_ethnicity_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_1/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_1/positivecovidtest_multivar3_withoutethn.ster"
# Sensitivity Analysis 1
# Remove people with antiplatelets
# Objective 1: compare AF treated people with general population
# Primary Outcomes: ONS COVID-19 death
SA1_02c_cr_create_population_af_match_onscoviddeath:
run: stata-mp:latest analysis/SA1_02c_cr_create_population.do onscoviddeath SA1_af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_onscoviddeath.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_onscoviddeath.dta"
data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_onscoviddeath.dta"
SA1_05c_an_models_af_match_onscoviddeath:
run: stata-mp:latest analysis/05c_an_models.do onscoviddeath SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_onscoviddeath, 05c_an_models_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/05c_an_models_onscoviddeath.log
table: "output/oac_match_tabfig/sens_analysis_1/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar3.ster"
SA1_06c_an_models_ethnicity_af_match_onscoviddeath:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do onscoviddeath SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_onscoviddeath, 06c_an_models_ethnicity_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_onscoviddeath.log
table: "output/oac_match_tabfig/sens_analysis_1/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_1/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA1_02c_cr_create_population_af_match_admitcovid:
run: stata-mp:latest analysis/SA1_02c_cr_create_population.do admitcovid SA1_af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_admitcovid.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_admitcovid.dta"
data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_admitcovid.dta"
SA1_05c_an_models_af_match_admitcovid:
run: stata-mp:latest analysis/05c_an_models.do admitcovid SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_admitcovid, 05c_an_models_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/05c_an_models_admitcovid.log
table: "output/oac_match_tabfig/sens_analysis_1/table2_admitcovid.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/admitcovid_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar3.ster"
SA1_06c_an_models_ethnicity_af_match_admitcovid:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do admitcovid SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_admitcovid, 06c_an_models_ethnicity_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_admitcovid.log
table: "output/oac_match_tabfig/sens_analysis_1/table3_admitcovid.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/admitcovid_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_1/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA1_02c_cr_create_population_af_match_covidtest:
run: stata-mp:latest analysis/SA1_02c_cr_create_population.do covidtest SA1_af_match
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_covidtest.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_covidtest.dta"
data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_covidtest.dta"
SA1_05c_an_models_af_match_covidtest:
run: stata-mp:latest analysis/05c_an_models.do covidtest SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_covidtest, 05c_an_models_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/05c_an_models_covidtest.log
table: "output/oac_match_tabfig/sens_analysis_1/table2_covidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/covidtest_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar3.ster"
SA1_06c_an_models_ethnicity_af_match_covidtest:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do covidtest SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_covidtest, 06c_an_models_ethnicity_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_covidtest.log
table: "output/oac_match_tabfig/sens_analysis_1/table3_covidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/covidtest_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_1/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA1_02c_cr_create_population_af_match_positivecovidtest:
run: stata-mp:latest analysis/SA1_02c_cr_create_population.do positivecovidtest SA1_af_match
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/SA1_02c_cr_create_population_positivecovidtest.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_positivecovidtest.dta"
data3: "output/oac_match_tempdata/sens_analysis_1/analysis_dataset_STSET_positivecovidtest.dta"
SA1_05c_an_models_af_match_positivecovidtest:
run: stata-mp:latest analysis/05c_an_models.do positivecovidtest SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_positivecovidtest, 05c_an_models_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/05c_an_models_positivecovidtest.log
table: "output/oac_match_tabfig/sens_analysis_1/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar3.ster"
SA1_06c_an_models_ethnicity_af_match_positivecovidtest:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do positivecovidtest SA1_af_match
needs: [SA1_02c_cr_create_population_af_match_positivecovidtest, 06c_an_models_ethnicity_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_1/06c_an_models_ethnicity_positivecovidtest.log
table: "output/oac_match_tabfig/sens_analysis_1/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_1/positivecovidtest_multivar3_withoutethn.ster"
# Sensitivity Analysis 2
# limit the study cohort to people who aged 55
# Objective 1: compare AF treated people with AF non-treated people
# Primary Outcomes: ONS COVID-19 death
SA2_02a_cr_create_population_af_oac_onscoviddeath:
run: stata-mp:latest analysis/SA2_02a_cr_create_population.do onscoviddeath SA2_af_oac
needs: [02aii_cr_create_population_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_onscoviddeath.dta"
data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_onscoviddeath.dta"
SA2_05a_an_models_af_oac_onscoviddeath:
run: stata-mp:latest analysis/05a_an_models.do onscoviddeath SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_onscoviddeath, 05a_an_models_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/05a_an_models_onscoviddeath.log
table: "output/oac_tabfig/sens_analysis_2/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/onscoviddeath_univar.ster"
data2: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar3.ster"
SA2_06a_an_models_ethnicity_af_oac_onscoviddeath:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do onscoviddeath SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_onscoviddeath, 06a_an_models_ethnicity_af_oac_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_onscoviddeath.log
table: "output/oac_tabfig/sens_analysis_2/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/onscoviddeath_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_2/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA2_02a_cr_create_population_af_oac_admitcovid:
run: stata-mp:latest analysis/SA2_02a_cr_create_population.do admitcovid SA2_af_oac
needs: [02aii_cr_create_population_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_admitcovid.dta"
data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_admitcovid.dta"
SA2_05a_an_models_af_oac_admitcovid:
run: stata-mp:latest analysis/05a_an_models.do admitcovid SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_admitcovid, 05a_an_models_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/05a_an_models_admitcovid.log
table: "output/oac_tabfig/sens_analysis_2/table2_admitcovid.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/admitcovid_univar.ster"
data2: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar3.ster"
SA2_06a_an_models_ethnicity_af_oac_admitcovid:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do admitcovid SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_admitcovid, 06a_an_models_ethnicity_af_oac_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_admitcovid.log
table: "output/oac_tabfig/sens_analysis_2/table3_admitcovid.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/admitcovid_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_2/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA2_02a_cr_create_population_af_oac_covidtest:
run: stata-mp:latest analysis/SA2_02a_cr_create_population.do covidtest SA2_af_oac
needs: [02aii_cr_create_population_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_covidtest.dta"
data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_covidtest.dta"
SA2_05a_an_models_af_oac_covidtest:
run: stata-mp:latest analysis/05a_an_models.do covidtest SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_covidtest, 05a_an_models_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/05a_an_models_covidtest.log
table: "output/oac_tabfig/sens_analysis_2/table2_covidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/covidtest_univar.ster"
data2: "output/oac_tempdata/sens_analysis_2/covidtest_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_2/covidtest_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_2/covidtest_multivar3.ster"
SA2_06a_an_models_ethnicity_af_oac_covidtest:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do covidtest SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_covidtest, 06a_an_models_ethnicity_af_oac_covidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_covidtest.log
table: "output/oac_tabfig/sens_analysis_2/table3_covidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/covidtest_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_2/covidtest_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_2/covidtest_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_2/covidtest_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_2/covidtest_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_2/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA2_02a_cr_create_population_af_oac_positivecovidtest:
run: stata-mp:latest analysis/SA2_02a_cr_create_population.do positivecovidtest SA2_af_oac
needs: [02aii_cr_create_population_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/SA2_02a_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/analysis_dataset_positivecovidtest.dta"
data2: "output/oac_tempdata/sens_analysis_2/analysis_dataset_STSET_positivecovidtest.dta"
SA2_05a_an_models_af_oac_positivecovidtest:
run: stata-mp:latest analysis/05a_an_models.do positivecovidtest SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_positivecovidtest, 05a_an_models_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/05a_an_models_positivecovidtest.log
table: "output/oac_tabfig/sens_analysis_2/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/positivecovidtest_univar.ster"
data2: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar1.ster"
data3: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar2.ster"
data4: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar3.ster"
SA2_06a_an_models_ethnicity_af_oac_positivecovidtest:
run: stata-mp:latest analysis/06a_an_models_ethnicity.do positivecovidtest SA2_af_oac
needs: [SA2_02a_cr_create_population_af_oac_positivecovidtest, 06a_an_models_ethnicity_af_oac_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_log/sens_analysis_2/06a_an_models_ethnicity_positivecovidtest.log
table: "output/oac_tabfig/sens_analysis_2/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_tempdata/sens_analysis_2/positivecovidtest_univar_ethn.ster"
data2: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar1_ethn.ster"
data3: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar2_ethn.ster"
data4: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar3_ethn.ster"
data6: "output/oac_tempdata/sens_analysis_2/positivecovidtest_multivar3_withoutethn.ster"
# Sensitivity Analysis 2
# limit the study cohort to people who aged 55
# Objective 1: compare AF treated people with general population
# Primary Outcomes: ONS COVID-19 death
SA2_02c_cr_create_population_af_match_onscoviddeath:
run: stata-mp:latest analysis/SA2_02c_cr_create_population.do onscoviddeath SA2_af_match
needs: [02c_cr_create_population_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_onscoviddeath.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_onscoviddeath.dta"
data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_onscoviddeath.dta"
SA2_05c_an_models_af_match_onscoviddeath:
run: stata-mp:latest analysis/05c_an_models.do onscoviddeath SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_onscoviddeath, 05c_an_models_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/05c_an_models_onscoviddeath.log
table: "output/oac_match_tabfig/sens_analysis_2/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar3.ster"
SA2_06c_an_models_ethnicity_af_match_onscoviddeath:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do onscoviddeath SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_onscoviddeath, 06c_an_models_ethnicity_af_match_onscoviddeath]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_onscoviddeath.log
table: "output/oac_match_tabfig/sens_analysis_2/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_2/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA2_02c_cr_create_population_af_match_admitcovid:
run: stata-mp:latest analysis/SA2_02c_cr_create_population.do admitcovid SA2_af_match
needs: [02c_cr_create_population_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_admitcovid.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_admitcovid.dta"
data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_admitcovid.dta"
SA2_05c_an_models_af_match_admitcovid:
run: stata-mp:latest analysis/05c_an_models.do admitcovid SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_admitcovid, 05c_an_models_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/05c_an_models_admitcovid.log
table: "output/oac_match_tabfig/sens_analysis_2/table2_admitcovid.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/admitcovid_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar3.ster"
SA2_06c_an_models_ethnicity_af_match_admitcovid:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do admitcovid SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_admitcovid, 06c_an_models_ethnicity_af_match_admitcovid]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_admitcovid.log
table: "output/oac_match_tabfig/sens_analysis_2/table3_admitcovid.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/admitcovid_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_2/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA2_02c_cr_create_population_af_match_covidtest:
run: stata-mp:latest analysis/SA2_02c_cr_create_population.do covidtest SA2_af_match
needs: [02c_cr_create_population_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_covidtest.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_covidtest.dta"
data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_covidtest.dta"
SA2_05c_an_models_af_match_covidtest:
run: stata-mp:latest analysis/05c_an_models.do covidtest SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_covidtest, 05c_an_models_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/05c_an_models_covidtest.log
table: "output/oac_match_tabfig/sens_analysis_2/table2_covidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/covidtest_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar3.ster"
SA2_06c_an_models_ethnicity_af_match_covidtest:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do covidtest SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_covidtest, 06c_an_models_ethnicity_af_match_covidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_covidtest.log
table: "output/oac_match_tabfig/sens_analysis_2/table3_covidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/covidtest_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_2/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA2_02c_cr_create_population_af_match_positivecovidtest:
run: stata-mp:latest analysis/SA2_02c_cr_create_population.do positivecovidtest SA2_af_match
needs: [02c_cr_create_population_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/SA2_02c_cr_create_population_positivecovidtest.log
highly_sensitive:
data2: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_positivecovidtest.dta"
data3: "output/oac_match_tempdata/sens_analysis_2/analysis_dataset_STSET_positivecovidtest.dta"
SA2_05c_an_models_af_match_positivecovidtest:
run: stata-mp:latest analysis/05c_an_models.do positivecovidtest SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_positivecovidtest, 05c_an_models_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/05c_an_models_positivecovidtest.log
table: "output/oac_match_tabfig/sens_analysis_2/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_univar.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar1.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar2.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar3.ster"
SA2_06c_an_models_ethnicity_af_match_positivecovidtest:
run: stata-mp:latest analysis/06c_an_models_ethnicity.do positivecovidtest SA2_af_match
needs: [SA2_02c_cr_create_population_af_match_positivecovidtest, 06c_an_models_ethnicity_af_match_positivecovidtest]
outputs:
moderately_sensitive:
log: output/oac_match_log/sens_analysis_2/06c_an_models_ethnicity_positivecovidtest.log
table: "output/oac_match_tabfig/sens_analysis_2/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_univar_ethn.ster"
data2: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar1_ethn.ster"
data3: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar2_ethn.ster"
data4: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar3_ethn.ster"
data6: "output/oac_match_tempdata/sens_analysis_2/positivecovidtest_multivar3_withoutethn.ster"
# Sensitivity Analysis 3
# Exclude people who were prescribed both warfarin and DOACs on the same day as the latest OAC prescription
# Objective 2: Compare warfarin users and DOAC users
# Primary Outcomes: ONS COVID-19 death
SA3_02b_cr_create_population_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/SA3_02b_cr_create_population.do onscoviddeath SA3_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_onscoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_onscoviddeath.dta"
SA3_05b_an_models_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/05b_an_models_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_3/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar3.ster"
SA3_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_3/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_3/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA3_02b_cr_create_population_af_warfarin_admitcovid:
run: stata-mp:latest analysis/SA3_02b_cr_create_population.do admitcovid SA3_af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_admitcovid.dta"
data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_admitcovid.dta"
SA3_05b_an_models_af_warfarin_admitcovid:
run: stata-mp:latest analysis/05b_an_models.do admitcovid SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/05b_an_models_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_3/table2_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/admitcovid_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar3.ster"
SA3_06b_an_models_ethnicity_af_warfarin_admitcovid:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_3/table3_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/admitcovid_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_3/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: Non-COVID death
SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/SA3_02b_cr_create_population.do onsnoncoviddeath SA3_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_onsnoncoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_onsnoncoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_onsnoncoviddeath.dta"
SA3_05b_an_models_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/05b_an_models_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_3/table2_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar3.ster"
SA3_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_3/table3_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_3/onsnoncoviddeath_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA3_02b_cr_create_population_af_warfarin_covidtest:
run: stata-mp:latest analysis/SA3_02b_cr_create_population.do covidtest SA3_af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_covidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_covidtest.dta"
SA3_05b_an_models_af_warfarin_covidtest:
run: stata-mp:latest analysis/05b_an_models.do covidtest SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/05b_an_models_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_3/table2_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/covidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar3.ster"
SA3_06b_an_models_ethnicity_af_warfarin_covidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_3/table3_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/covidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_3/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA3_02b_cr_create_population_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/SA3_02b_cr_create_population.do positivecovidtest SA3_af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/SA3_02b_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_positivecovidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_3/analysis_dataset_STSET_positivecovidtest.dta"
SA3_05b_an_models_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/05b_an_models_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_3/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar3.ster"
SA3_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA3_af_warfarin
needs: [SA3_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_3/06b_an_models_ethnicity_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_3/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_3/positivecovidtest_multivar3_withoutethn.ster"
# Sensitivity Analysis 4
# Exclude people who ever had warfarin prescription 4 months before cohort entry in the DOAC group
# Objective 2: Compare warfarin users and DOAC users
# Primary Outcomes: ONS COVID-19 death
SA4_02b_cr_create_population_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/SA4_02b_cr_create_population.do onscoviddeath SA4_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_onscoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_onscoviddeath.dta"
SA4_05b_an_models_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/05b_an_models_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_4/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar3.ster"
SA4_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_4/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_4/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA4_02b_cr_create_population_af_warfarin_admitcovid:
run: stata-mp:latest analysis/SA4_02b_cr_create_population.do admitcovid SA4_af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_admitcovid.dta"
data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_admitcovid.dta"
SA4_05b_an_models_af_warfarin_admitcovid:
run: stata-mp:latest analysis/05b_an_models.do admitcovid SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/05b_an_models_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_4/table2_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/admitcovid_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar3.ster"
SA4_06b_an_models_ethnicity_af_warfarin_admitcovid:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_4/table3_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/admitcovid_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_4/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: Non-COVID death
SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/SA4_02b_cr_create_population.do onsnoncoviddeath SA4_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_onsnoncoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_onsnoncoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_onsnoncoviddeath.dta"
SA4_05b_an_models_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/05b_an_models_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_4/table2_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar3.ster"
SA4_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_4/table3_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_4/onsnoncoviddeath_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA4_02b_cr_create_population_af_warfarin_covidtest:
run: stata-mp:latest analysis/SA4_02b_cr_create_population.do covidtest SA4_af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_covidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_covidtest.dta"
SA4_05b_an_models_af_warfarin_covidtest:
run: stata-mp:latest analysis/05b_an_models.do covidtest SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/05b_an_models_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_4/table2_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/covidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar3.ster"
SA4_06b_an_models_ethnicity_af_warfarin_covidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_4/table3_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/covidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_4/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA4_02b_cr_create_population_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/SA4_02b_cr_create_population.do positivecovidtest SA4_af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/SA4_02b_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_positivecovidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_4/analysis_dataset_STSET_positivecovidtest.dta"
SA4_05b_an_models_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/05b_an_models_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_4/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar3.ster"
SA4_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA4_af_warfarin
needs: [SA4_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_4/06b_an_models_ethnicity_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_4/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_4/positivecovidtest_multivar3_withoutethn.ster"
# Sensitivity Analysis 5
# Use time-updated exposure variable (warfarin/DOACs)
# Objective 2: Compare warfarin users and DOAC users
# Primary Outcomes: ONS COVID-19 death
SA5_02b_cr_create_population_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/SA5_02b_cr_create_population.do onscoviddeath SA5_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_onscoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/last_date_onscoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_onscoviddeath.dta"
data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_onscoviddeath.dta"
data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_onscoviddeath.dta"
data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_onscoviddeath.dta"
SA5_03b_an_checks:
run: stata-mp:latest analysis/SA5_03b_an_checks.do SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/SA5_03b_an_checks.log
SA5_05b_an_models_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onscoviddeath SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_onscoviddeath, 05b_an_models_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/05b_an_models_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_5/table2_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar3.ster"
SA5_06b_an_models_ethnicity_af_warfarin_onscoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onscoviddeath SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_onscoviddeath, 06b_an_models_ethnicity_af_warfarin_onscoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_onscoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_5/table3_onscoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_5/onscoviddeath_multivar3_withoutethn.ster"
# Primary Outcomes: COVID-19 hospital admission
SA5_02b_cr_create_population_af_warfarin_admitcovid:
run: stata-mp:latest analysis/SA5_02b_cr_create_population.do admitcovid SA5_af_warfarin
needs: [02b_cr_create_population_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_admitcovid.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/last_date_admitcovid.dta"
data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_admitcovid.dta"
data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_admitcovid.dta"
data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_admitcovid.dta"
data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_admitcovid.dta"
SA5_05b_an_models_af_warfarin_admitcovid:
run: stata-mp:latest analysis/05b_an_models.do admitcovid SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_admitcovid, 05b_an_models_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/05b_an_models_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_5/table2_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/admitcovid_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar3.ster"
SA5_06b_an_models_ethnicity_af_warfarin_admitcovid:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do admitcovid SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_admitcovid, 06b_an_models_ethnicity_af_warfarin_admitcovid]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_admitcovid.log
table: "output/warfarin_tabfig/sens_analysis_5/table3_admitcovid.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/admitcovid_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_5/admitcovid_multivar3_withoutethn.ster"
# Exploratory Outcomes: Non-COVID death
SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/SA5_02b_cr_create_population.do onsnoncoviddeath SA5_af_warfarin
needs: [02b_cr_create_population_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_onsnoncoviddeath.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/last_date_onsnoncoviddeath.dta"
data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_onsnoncoviddeath.dta"
data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_onsnoncoviddeath.dta"
data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_onsnoncoviddeath.dta"
data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_onsnoncoviddeath.dta"
SA5_05b_an_models_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/05b_an_models.do onsnoncoviddeath SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 05b_an_models_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/05b_an_models_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_5/table2_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar3.ster"
SA5_06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do onsnoncoviddeath SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_onsnoncoviddeath, 06b_an_models_ethnicity_af_warfarin_onsnoncoviddeath]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_onsnoncoviddeath.log
table: "output/warfarin_tabfig/sens_analysis_5/table3_onsnoncoviddeath.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_5/onsnoncoviddeath_multivar3_withoutethn.ster"
# Exploratory Outcomes: COVID-19 test
SA5_02b_cr_create_population_af_warfarin_covidtest:
run: stata-mp:latest analysis/SA5_02b_cr_create_population.do covidtest SA5_af_warfarin
needs: [02b_cr_create_population_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_covidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/last_date_covidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_covidtest.dta"
data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_covidtest.dta"
data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_covidtest.dta"
data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_covidtest.dta"
SA5_05b_an_models_af_warfarin_covidtest:
run: stata-mp:latest analysis/05b_an_models.do covidtest SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_covidtest, 05b_an_models_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/05b_an_models_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_5/table2_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/covidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar3.ster"
SA5_06b_an_models_ethnicity_af_warfarin_covidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do covidtest SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_covidtest, 06b_an_models_ethnicity_af_warfarin_covidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_covidtest.log
table: "output/warfarin_tabfig/sens_analysis_5/table3_covidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/covidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_5/covidtest_multivar3_withoutethn.ster"
# Exploratory Outcomes: Positive COVID test
SA5_02b_cr_create_population_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/SA5_02b_cr_create_population.do positivecovidtest SA5_af_warfarin
needs: [02b_cr_create_population_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/SA5_02b_cr_create_population_positivecovidtest.log
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/last_date_positivecovidtest.dta"
data2: "output/warfarin_tempdata/sens_analysis_5/warfarin_rx_positivecovidtest.dta"
data3: "output/warfarin_tempdata/sens_analysis_5/doac_rx_positivecovidtest.dta"
data4: "output/warfarin_tempdata/sens_analysis_5/oac_rx_positivecovidtest.dta"
data5: "output/warfarin_tempdata/sens_analysis_5/analysis_dataset_STSET_positivecovidtest.dta"
SA5_05b_an_models_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/05b_an_models.do positivecovidtest SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_positivecovidtest, 05b_an_models_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/05b_an_models_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_5/table2_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_univar.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar1.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar2.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar3.ster"
SA5_06b_an_models_ethnicity_af_warfarin_positivecovidtest:
run: stata-mp:latest analysis/06b_an_models_ethnicity.do positivecovidtest SA5_af_warfarin
needs: [SA5_02b_cr_create_population_af_warfarin_positivecovidtest, 06b_an_models_ethnicity_af_warfarin_positivecovidtest]
outputs:
moderately_sensitive:
log: output/warfarin_log/sens_analysis_5/06b_an_models_ethnicity_positivecovidtest.log
table: "output/warfarin_tabfig/sens_analysis_5/table3_positivecovidtest.txt"
highly_sensitive:
data1: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_univar_ethn.ster"
data2: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar1_ethn.ster"
data3: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar2_ethn.ster"
data4: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar2_withoutethn.ster"
data5: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar3_ethn.ster"
data6: "output/warfarin_tempdata/sens_analysis_5/positivecovidtest_multivar3_withoutethn.ster"
Timeline
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Created:
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Started:
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Finished:
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Runtime: 00:00:06
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
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Succeeded
- Backend
- TPP
- Requested by
- Angel Wong
- Branch
- SA5-check
- Force run dependencies
- No
- Git commit hash
- 75aa3b3
- Requested actions
-
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SA5_02b_cr_create_population_af_warfarin_onscoviddeath
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