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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
# generate_study_population:
# run: cohortextractor:latest generate_cohort --study-definition study_definition
# outputs:
# highly_sensitive:
# cohort: output/input.csv
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2
outputs:
highly_sensitive:
cohort: output/input_2.csv
# generate_study_population_cohort_check:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_flow_chart
# outputs:
# highly_sensitive:
# cohort: output/input_*.csv
# generate_study_population_codelist_check:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_codelist_check
# outputs:
# highly_sensitive:
# cohort: output/input_*.csv
# generate_study_population_vacc_check_anyTest:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc_check_anyTest
# outputs:
# highly_sensitive:
# cohort: output/input_vacc_check.csv
# generate_study_population_vacc_check_posTest:
# run: cohortextractor:latest generate_cohort --study-definition study_definition_vacc_check_posTest
# outputs:
# highly_sensitive:
# cohort: output/input_vacc_check_posTest.csv
# check_cohort:
# run: r:latest analysis/check_cohort.R
# needs: [generate_study_population_cohort_check]
# outputs:
# moderately_sensitive:
# cohort: output/check_cohort.csv
# check_codelist:
# run: r:latest analysis/check_codelist.R
# needs: [generate_study_population_codelist_check]
# outputs:
# moderately_sensitive:
# cohort: output/check_codelist.csv
# 4wk_onboarding:
# run: r:latest analysis/report.R
# needs: [generate_study_population]
# outputs:
# moderately_sensitive:
# n_patients: output/count_patients.csv
##cohort1: output/plot_postOp_mortality_30day.png
# subtable_table1_ageGroup: output/table1_ageGroup.csv
# subtable_table1_Sex: output/table1_Sex.csv
# subtable_table1_30dayMortality: output/table1_postOp_mortality_30day.csv
# table1_df_4wk: output/table1_4wk_onboarding.csv
##table1_kable_4wk: output/Table1_4wk_onboarding.png
# subtable_table1_ageGroup_3mths: output/table1_ageGroup_3mths.csv
# subtable_table1_Sex_3mths: output/table1_Sex_3mths.csv
# subtable_table1_30dayMortality_3mths: output/table1_postOp_mortality_30day_3mths.csv
# table1_df_4wk_3mths: output/table1_4wk_onboarding_3mths.csv
##table1_kable_4wk_3mths: output/Table1_4wk_onboarding_3mths.png
# subtable_table1_ageGroup_6mths: output/table1_ageGroup_6mths.csv
# subtable_table1_Sex_6mths: output/table1_Sex_6mths.csv
# subtable_table1_30dayMortality_6mths: output/table1_postOp_mortality_30day_6mths.csv
# table1_df_4wk_6mths: output/table1_4wk_onboarding_6mths.csv
##table1_kable_4wk_6mths: output/Table1_4wk_onboarding_6mths.png
# tableVacc_30dayMortality: output/tableVacc_postOp_mortality_30day.csv
# tableVacc_df: output/table_Vaccination_status.csv
##tableVacc_kable: output/TableVacc.png
# tableVacc_30dayMortality_3mths: output/tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_df_3mths: output/table_Vaccination_status_3mths.csv
##tableVacc_kable_3mths: output/TableVacc_3mths.png
# tableVacc_30dayMortality_6mths: output/tableVacc_postOp_mortality_30day_6mths.csv
# tableVacc_df_6mths: output/table_Vaccination_status_6mths.csv
##tableVacc_kable_6mths: output/TableVacc_6mths.png
# vacc_definition_check_anyTest:
# run: r:latest analysis/vacc_check.R
# needs: [generate_study_population_vacc_check_anyTest]
# outputs:
# moderately_sensitive:
# tableVacc_30dayMortality_3mths_SNOMED: output/SNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_TPP: output/TPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynSNOMED: output/AlwynSNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynTPP: output/AlwynTPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_df_check_3mths_SNOMED: output/SNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_TPP: output/TPP_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynSNOMED: output/AlwynSNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynTPP: output/AlwynTPP_table_Vaccination_status_3mths.csv
# vacc_definition_check_posTest:
# run: r:latest analysis/vacc_check.R
# needs: [generate_study_population_vacc_check_posTest]
# outputs:
# moderately_sensitive:
# tableVacc_30dayMortality_3mths_SNOMED: output/SNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_TPP: output/TPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynSNOMED: output/AlwynSNOMED_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_30dayMortality_3mths_AlwynTPP: output/AlwynTPP_tableVacc_postOp_mortality_30day_3mths.csv
# tableVacc_df_check_3mths_SNOMED: output/SNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_TPP: output/TPP_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynSNOMED: output/AlwynSNOMED_table_Vaccination_status_3mths.csv
# tableVacc_df_check_3mths_AlwynTPP: output/AlwynTPP_table_Vaccination_status_3mths.csv
COVIDSurg_compare:
run: r:latest analysis/Make_table_COVIDSurg_compare.R
needs: [generate_study_population_2]
outputs:
moderately_sensitive:
table_counts: output/table_Count_of_patients_in_each_cohort_in_each_era_across_all_intervals.csv
table_counts_7wkThreshold: output/table_7wkThreshold_Count_of_patients_in_each_cohort_in_each_era_across_all_intervals.csv
table_mortality_intervals: output/table_30day_post-op_mortality_in_each_era_across_all_intervals.csv
table_mortality_intervals_7wkThreshold: output/table_7wkThreshold_30day_post-op_mortality_in_each_era_across_all_intervals.csv
table_mortality_totals: output/table_30day_post-op_mortality_for_each_cohort_in_each_era.csv
plotData_C3m: output/plotData_C3m.csv
plotData_C6m: output/plotData_C6m.csv
plotData_NC: output/plotData_NC.csv
plotData_AdmMethod: output/plotData_AdmMethod.csv
figure_NC_3m: output/noCancer__3monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_NC_2m: output/noCancer__2monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_NC_1m: output/noCancer__1monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_NC_wk: output/noCancer__weekly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C3m_3m: output/cancer_3months__3monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C3m_2m: output/cancer_3months__2monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C3m_1m: output/cancer_3months__1monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C3m_wk: output/cancer_3months__weekly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C6m_3m: output/cancer_6months__3monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C6m_2m: output/cancer_6months__2monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C6m_1m: output/cancer_6months__1monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_C6m_wk: output/cancer_6months__weekly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_AdmMethod_3m: output/noCancer__stratified_3monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_AdmMethod_2m: output/noCancer__stratified_2monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_AdmMethod_1m: output/noCancer__stratified_1monthly_summary_proportion_surgeries_within_7wks_after_pos_test.png
figure_AdmMethod_wk: output/noCancer__stratified_weekly_summary_proportion_surgeries_within_7wks_after_pos_test.png
emulate_table1:
run: r:latest analysis/Make_all_Table1s.R
needs: [generate_study_population_2]
outputs:
moderately_sensitive:
table1Demogs_PP_EntireSurgeryCohort: output/table1Demogs_PP_EntireSurgeryCohort.csv
table1Outcomes_PP_EntireSurgeryCohort: output/table1Outcomes_PP_EntireSurgeryCohort.csv
table1Demogs_CSP_EntireSurgeryCohort: output/table1Demogs_CSP_EntireSurgeryCohort.csv
table1Outcomes_CSP_EntireSurgeryCohort: output/table1Outcomes_CSP_EntireSurgeryCohort.csv
table1Demogs_PNV_EntireSurgeryCohort: output/table1Demogs_PNV_EntireSurgeryCohort.csv
table1Outcomes_PNV_EntireSurgeryCohort: output/table1Outcomes_PNV_EntireSurgeryCohort.csv
table1Demogs_PWV_EntireSurgeryCohort: output/table1Demogs_PWV_EntireSurgeryCohort.csv
table1Outcomes_PWV_EntireSurgeryCohort: output/table1Outcomes_PWV_EntireSurgeryCohort.csv
table1Demogs_PP_3mths: output/table1Demogs_PP_3mths.csv
table1Outcomes_PP_3mths: output/table1Outcomes_PP_3mths.csv
table1Demogs_CSP_3mths: output/table1Demogs_CSP_3mths.csv
table1Outcomes_CSP_3mths: output/table1Outcomes_CSP_3mths.csv
table1Demogs_PNV_3mths: output/table1Demogs_PNV_3mths.csv
table1Outcomes_PNV_3mths: output/table1Outcomes_PNV_3mths.csv
table1Demogs_PWV_3mths: output/table1Demogs_PWV_3mths.csv
table1Outcomes_PWV_3mths: output/table1Outcomes_PWV_3mths.csv
table1Demogs_PP_6mths: output/table1Demogs_PP_6mths.csv
table1Outcomes_PP_6mths: output/table1Outcomes_PP_6mths.csv
table1Demogs_CSP_6mths: output/table1Demogs_CSP_6mths.csv
table1Outcomes_CSP_6mths: output/table1Outcomes_CSP_6mths.csv
table1Demogs_PNV_6mths: output/table1Demogs_PNV_6mths.csv
table1Outcomes_PNV_6mths: output/table1Outcomes_PNV_6mths.csv
table1Demogs_PWV_6mths: output/table1Demogs_PWV_6mths.csv
table1Outcomes_PWV_6mths: output/table1Outcomes_PWV_6mths.csv
table1Demogs_CSP_7wkThreshold: output/table1Demogs_CSP_EntireSurgeryCohort_7wkThreshold.csv
table1Outcomes_CSP_7wkThreshold: output/table1Outcomes_CSP_EntireSurgeryCohort_7wkThreshold.csv
table1Demogs_PNV_7wkThreshold: output/table1Demogs_PNV_EntireSurgeryCohort_7wkThreshold.csv
table1Outcomes_PNV_7wkThreshold: output/table1Outcomes_PNV_EntireSurgeryCohort_7wkThreshold.csv
table1Demogs_PWV_7wkThreshold: output/table1Demogs_PWV_EntireSurgeryCohort_7wkThreshold.csv
table1Outcomes_PWV_7wkThreshold: output/table1Outcomes_PWV_EntireSurgeryCohort_7wkThreshold.csv
table1Demogs_CSP_3mths_7wkThreshold: output/table1Demogs_CSP_3mths_7wkThreshold.csv
table1Outcomes_CSP_3mths_7wkThreshold: output/table1Outcomes_CSP_3mths_7wkThreshold.csv
table1Demogs_PNV_3mths_7wkThreshold: output/table1Demogs_PNV_3mths_7wkThreshold.csv
table1Outcomes_PNV_3mths_7wkThreshold: output/table1Outcomes_PNV_3mths_7wkThreshold.csv
table1Demogs_PWV_3mths_7wkThreshold: output/table1Demogs_PWV_3mths_7wkThreshold.csv
table1Outcomes_PWV_3mths_7wkThreshold: output/table1Outcomes_PWV_3mths_7wkThreshold.csv
table1Demogs_CSP_6mths_7wkThreshold: output/table1Demogs_CSP_6mths_7wkThreshold.csv
table1Outcomes_CSP_6mths_7wkThreshold: output/table1Outcomes_CSP_6mths_7wkThreshold.csv
table1Demogs_PNV_6mths_7wkThreshold: output/table1Demogs_PNV_6mths_7wkThreshold.csv
table1Outcomes_PNV_6mths_7wkThreshold: output/table1Outcomes_PNV_6mths_7wkThreshold.csv
table1Demogs_PWV_6mths_7wkThreshold: output/table1Demogs_PWV_6mths_7wkThreshold.csv
table1Outcomes_PWV_6mths_7wkThreshold: output/table1Outcomes_PWV_6mths_7wkThreshold.csv
output_for_publication:
run: r:latest analysis/Tables_for_1st_publication.R
needs: [generate_study_population_2]
outputs:
moderately_sensitive:
table1Demogs_PP: output/table1Demogs_PP.csv
table1Demogs_PNV: output/table1Demogs_PNV.csv
table1Demogs_CSP: output/table1Demogs_CSP.csv
table1Demogs_PWV: output/table1Demogs_PWV.csv
table1Outcomes_PP: output/table1Outcomes_PP.csv
table1Outcomes_PNV: output/table1Outcomes_PNV.csv
table1Outcomes_CSP: output/table1Outcomes_CSP.csv
table1Outcomes_PWV: output/table1Outcomes_PWV.csv
TableEra: output/TableEra.csv