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project.yaml
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project.yaml
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version: "3.0"
expectations:
population_size: 100000
actions:
generate_cohorts:
run: cohortextractor:latest generate_cohort --study-definition study_definition
outputs:
highly_sensitive:
cohort: output/input.csv
crmain:
run: stata-mp:latest analysis/01_eth_cr_analysis_dataset.do
needs: [generate_cohorts]
outputs:
highly_sensitive:
data: output/analysis_dataset.dta
moderately_sensitive:
log: logs/01_eth_cr_analysis_dataset.log
cr_sgss:
run: stata-mp:latest analysis/01b_eth_cr_stset_sgss.do
needs: [crmain]
outputs:
highly_sensitive:
stsettested: output/analysis_dataset_STSET_tested.dta
stsetpositiivetest: output/analysis_dataset_STSET_positivetest.dta
moderately_sensitive:
log: logs/01b_eth_cr_stset_sgss.log
cr_hes_covid:
run: stata-mp:latest analysis/01c_eth_cr_stset_hes.do
needs: [crmain]
outputs:
highly_sensitive:
stsethes: output/analysis_dataset_STSET_hes.dta
stseticu: output/analysis_dataset_STSET_icu.dta
stsetonscoviddeath: output/analysis_dataset_STSET_onscoviddeath.dta
moderately_sensitive:
log: logs/01c_eth_cr_stset_hes_covid.log
cr_ons:
run: stata-mp:latest analysis/01d_eth_cr_stset_death.do
needs: [crmain]
outputs:
highly_sensitive:
stsetons_noncoviddeath: output/analysis_dataset_STSET_ons_noncoviddeath.dta
stsetonsdeath: output/analysis_dataset_STSET_onsdeath.dta
moderately_sensitive:
log: logs/01d_eth_cr_stset_death.log
cr_confirmed:
run: stata-mp:latest analysis/01e_eth_cr_stset_confirmedcovid.do
needs: [crmain]
outputs:
highly_sensitive:
stset_onsconfirmeddeath: output/analysis_dataset_STSET_onsconfirmeddeath.dta
moderately_sensitive:
log: logs/01e_eth_cr_stset_onsconfirmeddeath.log
cr_underlying:
run: stata-mp:latest analysis/01f_eth_cr_stset_underlyingcovid.do
needs: [crmain]
outputs:
highly_sensitive:
stset_onsconfirmeddeath: output/analysis_dataset_STSET_onsunderlyingdeath.dta
moderately_sensitive:
log: logs/01e_eth_cr_stset_onsunderlyingdeath.log
check_region:
run: stata-mp:latest analysis/02b_eth_region_check.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/02b_region_check.log
table: output/table0_region.txt
check_tested:
run: stata-mp:latest analysis/21_eth_tested_characteristics.do
needs: [crmain]
outputs:
moderately_sensitive:
table: output/table1_tested.txt
main_carehomes_eth5:
run: stata-mp:latest analysis/06b_eth_an_multivariable_eth5_carehomesonly.do
needs: [cr_hes_covid]
outputs:
moderately_sensitive:
log: logs/06b_eth_an_hes_eth5_carehomesonly.log
table: output/table2_hes_eth5_carehomesonly.txt
estout: output/estout_table2_hes_eth5_carehomesonly.txt
graph: output/FP_hes_eth5_carehomesonly.txt
sens_nostp_eth16:
run: stata-mp:latest analysis/07a_eth_sensanalysis_nostp_eth16.do
needs: [cr_sgss, cr_hes_covid, cr_ons]
outputs:
moderately_sensitive:
log: logs/07a_eth_sensanalysis_nostp_eth16.log
table: output/sens_nostp_eth16.txt
estout: output/estout_sens_nostp_eth16.txt
graph: output/FP_sens_nostp_eth16.txt
sens_nostp_eth5:
run: stata-mp:latest analysis/07b_eth_sensanalysis_nostp_eth5.do
needs: [cr_sgss, cr_hes_covid, cr_ons]
outputs:
moderately_sensitive:
log: logs/07b_eth_sensanalysis_nostp_eth5.log
table: output/sens_nostp_eth5.txt
estout: output/estout_sens_nostp_eth5.txt
graph: output/FP_sens_nostp_eth5.txt
sens_ruralurban_eth16:
run: stata-mp:latest analysis/07c_eth_sensanalysis_ruralurban_eth16.do
needs: [cr_sgss, cr_hes_covid, cr_ons]
outputs:
moderately_sensitive:
log: logs/07c_eth_sensanalysis_ruralurban_eth16.log
estout: output/estout_sens_ruralurban_eth16.txt
sens_confirmed_eth16:
run: stata-mp:latest analysis/06c_eth_sensanalysis_confirmedcovid_eth16.do
needs: [cr_confirmed]
outputs:
moderately_sensitive:
log: logs/06c_sens_onsconfirmeddeath_eth16.log
estout: output/estout_onsconfirmeddeath_eth16.txt
graph: output/FP_sens_onsconfirmeddeath_eth16.txt
sens_confirmed_eth5:
run: stata-mp:latest analysis/06d_eth_sensanalysis_confirmedcovid_eth5.do
needs: [cr_confirmed]
outputs:
moderately_sensitive:
log: logs/06d_sens_onsconfirmeddeath_eth5.log
estout: output/estout_onsconfirmeddeath_eth5.txt
graph: output/FP_sens_onsconfirmeddeath_eth5.txt
sens_underlying_eth16:
run: stata-mp:latest analysis/06f_eth_sensanalysis_underlyingcovid_eth16.do
needs: [cr_underlying]
outputs:
moderately_sensitive:
log: logs/06f_sens_onsunderlyingdeath_eth16.log
estout: output/estout_onsunderlyingdeath_eth16.txt
graph: output/FP_sens_onsunderlyingdeath_eth16.txt
sens_underying_eth5:
run: stata-mp:latest analysis/06e_eth_sensanalysis_underlyingcovid_eth5.do
needs: [cr_underlying]
outputs:
moderately_sensitive:
log: logs/06e_sens_onsunderlyingdeath_eth5.log
estout: output/estout_onsunderlyingdeath_eth5.txt
graph: output/FP_sens_onsunderlyingdeath_eth5.txt
main_eth16_testedpop:
run: stata-mp:latest analysis/11a_eth_an_testedpop_eth16_nocarehomes.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/11a_eth_an_testedpop_eth16.log
table: output/table3_testedpop_eth16_nocarehomes.txt
estout: output/estout_table3_testedpop_eth16_nocarehomes.txt
graph: output/FP_testedpop_eth16.txt
main_eth5_testedpop:
run: stata-mp:latest analysis/11b_eth_an_testedpop_eth5_nocarehomes.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/11b_eth_an_testedpop_eth5.log
table: output/table3_testedpop_eth5_nocarehomes.txt
estout: output/estout_table3_testedpop_eth5_nocarehomes.txt
graph: output/FP_testedpop_eth5.txt
main_eth16_infectedpop:
run: stata-mp:latest analysis/12a_eth_an_infectedpop_eth16_nocarehomes.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/12a_eth_an_infectedpop_eth16.log
table: output/table4_infectedpop_eth16_nocarehomes.txt
estout: output/estout_table4_infectedpop_eth16_nocarehomes.txt
graph: output/FP_infectedpop_eth16.txt
main_eth5_infectedpop:
run: stata-mp:latest analysis/12b_eth_an_infectedpop_eth5_nocarehomes.do
needs: [crmain]
outputs:
moderately_sensitive:
log: logs/12b_eth_an_infectedpop_eth5.log
table: output/table4_infectedpop_eth5_nocarehomes.txt
estout: output/estout_table4_infectedpop_eth5_nocarehomes.txt
graph: output/FP_infectedpop_eth5.txt
check_ph:
run: stata-mp:latest analysis/20_eth_an_model_checks.do
needs: [cr_sgss, cr_hes_covid, cr_ons]
outputs:
moderately_sensitive:
table: output/Table_phtest_eth5.txt
graph1: output/kmplots_combined.svg
graph2: output/stphplots_combined.svg