generated from opensafely/research-template
/
project.yaml
1055 lines (948 loc) · 32.9 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 1000
actions:
## # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml DIRECTLY
## This file is created by create-project.R
## Edit and run create-project.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Pre-server scripts
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Extract and tidy
## # # # # # # # # # # # # # # # # # # #
extract:
run: cohortextractor:latest generate_cohort --study-definition study_definition
--output-format feather
needs: []
outputs:
highly_sensitive:
cohort: output/input.feather
data_process:
run: r:latest analysis/data_process.R
needs:
- extract
outputs:
highly_sensitive:
rds: output/data/data_processed.rds
vaxlong: output/data/data_vaxlong.rds
skim_process:
run: r:latest analysis/data_skim.R output/data/data_processed.rds output/data_properties
needs:
- data_process
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed*.txt
data_selection:
run: r:latest analysis/data_selection.R
needs:
- data_process
outputs:
highly_sensitive:
feather: output/data/data_cohort.feather
cohortrds: output/data/data_cohort.rds
criteriards: output/data/data_inclusioncriteria.rds
moderately_sensitive:
flow: output/data/flowchart.csv
skim_selection:
run: r:latest analysis/data_skim.R output/data/data_cohort.rds output/data_properties
needs:
- data_selection
outputs:
moderately_sensitive:
cohort: output/data_properties/data_cohort*.txt
geography:
run: r:latest analysis/geography.R
needs:
- data_process
outputs:
moderately_sensitive:
png: output/geography/*.png
csv: output/geography/*.csv
## # # # # # # # # # # # # # # # # # # #
## matching set A
## # # # # # # # # # # # # # # # # # # #
match_A:
run: r:latest analysis/match.R A
needs:
- data_selection
outputs:
highly_sensitive:
rds: output/match/A/*.rds
moderately_sensitive:
txt: output/match/A/*.txt
match_report_A:
run: r:latest analysis/match_report.R A
needs:
- data_selection
- match_A
outputs:
moderately_sensitive:
txt: output/match/A/report/*.txt
csv: output/match/A/report/*.csv
png: output/match/A/report/*.png
html: output/match/A/report/*.html
## ### Overall models (''all'')
km_A_all_postest:
run: r:latest analysis/km.R A all postest
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/all/postest/*.txt
csv: output/match/A/km/all/postest/*.csv
png: output/match/A/km/all/postest/*.png
km_A_all_covidemergency:
run: r:latest analysis/km.R A all covidemergency
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/all/covidemergency/*.txt
csv: output/match/A/km/all/covidemergency/*.csv
png: output/match/A/km/all/covidemergency/*.png
km_A_all_covidadmittedproxy1:
run: r:latest analysis/km.R A all covidadmittedproxy1
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/all/covidadmittedproxy1/*.txt
csv: output/match/A/km/all/covidadmittedproxy1/*.csv
png: output/match/A/km/all/covidadmittedproxy1/*.png
km_A_all_covidadmitted:
run: r:latest analysis/km.R A all covidadmitted
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/all/covidadmitted/*.txt
csv: output/match/A/km/all/covidadmitted/*.csv
png: output/match/A/km/all/covidadmitted/*.png
km_A_all_coviddeath:
run: r:latest analysis/km.R A all coviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/all/coviddeath/*.txt
csv: output/match/A/km/all/coviddeath/*.csv
png: output/match/A/km/all/coviddeath/*.png
km_A_all_noncoviddeath:
run: r:latest analysis/km.R A all noncoviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/all/noncoviddeath/*.txt
csv: output/match/A/km/all/noncoviddeath/*.csv
png: output/match/A/km/all/noncoviddeath/*.png
## ### Models by primary course (''vax12_type'')
km_A_vax12_type_postest:
run: r:latest analysis/km.R A vax12_type postest
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/vax12_type/postest/*.txt
csv: output/match/A/km/vax12_type/postest/*.csv
png: output/match/A/km/vax12_type/postest/*.png
km_A_vax12_type_covidemergency:
run: r:latest analysis/km.R A vax12_type covidemergency
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/vax12_type/covidemergency/*.txt
csv: output/match/A/km/vax12_type/covidemergency/*.csv
png: output/match/A/km/vax12_type/covidemergency/*.png
km_A_vax12_type_covidadmittedproxy1:
run: r:latest analysis/km.R A vax12_type covidadmittedproxy1
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/vax12_type/covidadmittedproxy1/*.txt
csv: output/match/A/km/vax12_type/covidadmittedproxy1/*.csv
png: output/match/A/km/vax12_type/covidadmittedproxy1/*.png
km_A_vax12_type_covidadmitted:
run: r:latest analysis/km.R A vax12_type covidadmitted
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/vax12_type/covidadmitted/*.txt
csv: output/match/A/km/vax12_type/covidadmitted/*.csv
png: output/match/A/km/vax12_type/covidadmitted/*.png
km_A_vax12_type_coviddeath:
run: r:latest analysis/km.R A vax12_type coviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/vax12_type/coviddeath/*.txt
csv: output/match/A/km/vax12_type/coviddeath/*.csv
png: output/match/A/km/vax12_type/coviddeath/*.png
km_A_vax12_type_noncoviddeath:
run: r:latest analysis/km.R A vax12_type noncoviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/vax12_type/noncoviddeath/*.txt
csv: output/match/A/km/vax12_type/noncoviddeath/*.csv
png: output/match/A/km/vax12_type/noncoviddeath/*.png
## ### Models by clinically vulnerable group (''cev_cv'')
km_A_cev_cv_postest:
run: r:latest analysis/km.R A cev_cv postest
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/cev_cv/postest/*.txt
csv: output/match/A/km/cev_cv/postest/*.csv
png: output/match/A/km/cev_cv/postest/*.png
km_A_cev_cv_covidemergency:
run: r:latest analysis/km.R A cev_cv covidemergency
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/cev_cv/covidemergency/*.txt
csv: output/match/A/km/cev_cv/covidemergency/*.csv
png: output/match/A/km/cev_cv/covidemergency/*.png
km_A_cev_cv_covidadmittedproxy1:
run: r:latest analysis/km.R A cev_cv covidadmittedproxy1
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/cev_cv/covidadmittedproxy1/*.txt
csv: output/match/A/km/cev_cv/covidadmittedproxy1/*.csv
png: output/match/A/km/cev_cv/covidadmittedproxy1/*.png
km_A_cev_cv_covidadmitted:
run: r:latest analysis/km.R A cev_cv covidadmitted
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/cev_cv/covidadmitted/*.txt
csv: output/match/A/km/cev_cv/covidadmitted/*.csv
png: output/match/A/km/cev_cv/covidadmitted/*.png
km_A_cev_cv_coviddeath:
run: r:latest analysis/km.R A cev_cv coviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/cev_cv/coviddeath/*.txt
csv: output/match/A/km/cev_cv/coviddeath/*.csv
png: output/match/A/km/cev_cv/coviddeath/*.png
km_A_cev_cv_noncoviddeath:
run: r:latest analysis/km.R A cev_cv noncoviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/cev_cv/noncoviddeath/*.txt
csv: output/match/A/km/cev_cv/noncoviddeath/*.csv
png: output/match/A/km/cev_cv/noncoviddeath/*.png
## ### Models by prior infection (''prior_covid_infection'')
km_A_prior_covid_infection_postest:
run: r:latest analysis/km.R A prior_covid_infection postest
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/prior_covid_infection/postest/*.txt
csv: output/match/A/km/prior_covid_infection/postest/*.csv
png: output/match/A/km/prior_covid_infection/postest/*.png
km_A_prior_covid_infection_covidemergency:
run: r:latest analysis/km.R A prior_covid_infection covidemergency
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/prior_covid_infection/covidemergency/*.txt
csv: output/match/A/km/prior_covid_infection/covidemergency/*.csv
png: output/match/A/km/prior_covid_infection/covidemergency/*.png
km_A_prior_covid_infection_covidadmittedproxy1:
run: r:latest analysis/km.R A prior_covid_infection covidadmittedproxy1
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/prior_covid_infection/covidadmittedproxy1/*.txt
csv: output/match/A/km/prior_covid_infection/covidadmittedproxy1/*.csv
png: output/match/A/km/prior_covid_infection/covidadmittedproxy1/*.png
km_A_prior_covid_infection_covidadmitted:
run: r:latest analysis/km.R A prior_covid_infection covidadmitted
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/prior_covid_infection/covidadmitted/*.txt
csv: output/match/A/km/prior_covid_infection/covidadmitted/*.csv
png: output/match/A/km/prior_covid_infection/covidadmitted/*.png
km_A_prior_covid_infection_coviddeath:
run: r:latest analysis/km.R A prior_covid_infection coviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/prior_covid_infection/coviddeath/*.txt
csv: output/match/A/km/prior_covid_infection/coviddeath/*.csv
png: output/match/A/km/prior_covid_infection/coviddeath/*.png
km_A_prior_covid_infection_noncoviddeath:
run: r:latest analysis/km.R A prior_covid_infection noncoviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/prior_covid_infection/noncoviddeath/*.txt
csv: output/match/A/km/prior_covid_infection/noncoviddeath/*.csv
png: output/match/A/km/prior_covid_infection/noncoviddeath/*.png
## ### Models by age (''age65plus'')
km_A_age65plus_postest:
run: r:latest analysis/km.R A age65plus postest
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/age65plus/postest/*.txt
csv: output/match/A/km/age65plus/postest/*.csv
png: output/match/A/km/age65plus/postest/*.png
km_A_age65plus_covidemergency:
run: r:latest analysis/km.R A age65plus covidemergency
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/age65plus/covidemergency/*.txt
csv: output/match/A/km/age65plus/covidemergency/*.csv
png: output/match/A/km/age65plus/covidemergency/*.png
km_A_age65plus_covidadmittedproxy1:
run: r:latest analysis/km.R A age65plus covidadmittedproxy1
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/age65plus/covidadmittedproxy1/*.txt
csv: output/match/A/km/age65plus/covidadmittedproxy1/*.csv
png: output/match/A/km/age65plus/covidadmittedproxy1/*.png
km_A_age65plus_covidadmitted:
run: r:latest analysis/km.R A age65plus covidadmitted
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/age65plus/covidadmitted/*.txt
csv: output/match/A/km/age65plus/covidadmitted/*.csv
png: output/match/A/km/age65plus/covidadmitted/*.png
km_A_age65plus_coviddeath:
run: r:latest analysis/km.R A age65plus coviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/age65plus/coviddeath/*.txt
csv: output/match/A/km/age65plus/coviddeath/*.csv
png: output/match/A/km/age65plus/coviddeath/*.png
km_A_age65plus_noncoviddeath:
run: r:latest analysis/km.R A age65plus noncoviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/age65plus/noncoviddeath/*.txt
csv: output/match/A/km/age65plus/noncoviddeath/*.csv
png: output/match/A/km/age65plus/noncoviddeath/*.png
## ### Models by variant era (''variantera'')
km_A_variantera_postest:
run: r:latest analysis/km.R A variantera postest
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/variantera/postest/*.txt
csv: output/match/A/km/variantera/postest/*.csv
png: output/match/A/km/variantera/postest/*.png
km_A_variantera_covidemergency:
run: r:latest analysis/km.R A variantera covidemergency
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/variantera/covidemergency/*.txt
csv: output/match/A/km/variantera/covidemergency/*.csv
png: output/match/A/km/variantera/covidemergency/*.png
km_A_variantera_covidadmittedproxy1:
run: r:latest analysis/km.R A variantera covidadmittedproxy1
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/variantera/covidadmittedproxy1/*.txt
csv: output/match/A/km/variantera/covidadmittedproxy1/*.csv
png: output/match/A/km/variantera/covidadmittedproxy1/*.png
km_A_variantera_covidadmitted:
run: r:latest analysis/km.R A variantera covidadmitted
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/variantera/covidadmitted/*.txt
csv: output/match/A/km/variantera/covidadmitted/*.csv
png: output/match/A/km/variantera/covidadmitted/*.png
km_A_variantera_coviddeath:
run: r:latest analysis/km.R A variantera coviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/variantera/coviddeath/*.txt
csv: output/match/A/km/variantera/coviddeath/*.csv
png: output/match/A/km/variantera/coviddeath/*.png
km_A_variantera_noncoviddeath:
run: r:latest analysis/km.R A variantera noncoviddeath
needs:
- match_A
- data_selection
outputs:
moderately_sensitive:
txt: output/match/A/km/variantera/noncoviddeath/*.txt
csv: output/match/A/km/variantera/noncoviddeath/*.csv
png: output/match/A/km/variantera/noncoviddeath/*.png
## # # # # # # # # # # # # # # # # # # #
## matching set B
## # # # # # # # # # # # # # # # # # # #
match_B:
run: r:latest analysis/match.R B
needs:
- data_selection
outputs:
highly_sensitive:
rds: output/match/B/*.rds
moderately_sensitive:
txt: output/match/B/*.txt
match_report_B:
run: r:latest analysis/match_report.R B
needs:
- data_selection
- match_B
outputs:
moderately_sensitive:
txt: output/match/B/report/*.txt
csv: output/match/B/report/*.csv
png: output/match/B/report/*.png
html: output/match/B/report/*.html
## ### Overall models (''all'')
km_B_all_postest:
run: r:latest analysis/km.R B all postest
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/all/postest/*.txt
csv: output/match/B/km/all/postest/*.csv
png: output/match/B/km/all/postest/*.png
km_B_all_covidemergency:
run: r:latest analysis/km.R B all covidemergency
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/all/covidemergency/*.txt
csv: output/match/B/km/all/covidemergency/*.csv
png: output/match/B/km/all/covidemergency/*.png
km_B_all_covidadmittedproxy1:
run: r:latest analysis/km.R B all covidadmittedproxy1
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/all/covidadmittedproxy1/*.txt
csv: output/match/B/km/all/covidadmittedproxy1/*.csv
png: output/match/B/km/all/covidadmittedproxy1/*.png
km_B_all_covidadmitted:
run: r:latest analysis/km.R B all covidadmitted
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/all/covidadmitted/*.txt
csv: output/match/B/km/all/covidadmitted/*.csv
png: output/match/B/km/all/covidadmitted/*.png
km_B_all_coviddeath:
run: r:latest analysis/km.R B all coviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/all/coviddeath/*.txt
csv: output/match/B/km/all/coviddeath/*.csv
png: output/match/B/km/all/coviddeath/*.png
km_B_all_noncoviddeath:
run: r:latest analysis/km.R B all noncoviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/all/noncoviddeath/*.txt
csv: output/match/B/km/all/noncoviddeath/*.csv
png: output/match/B/km/all/noncoviddeath/*.png
## ### Models by primary course (''vax12_type'')
km_B_vax12_type_postest:
run: r:latest analysis/km.R B vax12_type postest
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/vax12_type/postest/*.txt
csv: output/match/B/km/vax12_type/postest/*.csv
png: output/match/B/km/vax12_type/postest/*.png
km_B_vax12_type_covidemergency:
run: r:latest analysis/km.R B vax12_type covidemergency
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/vax12_type/covidemergency/*.txt
csv: output/match/B/km/vax12_type/covidemergency/*.csv
png: output/match/B/km/vax12_type/covidemergency/*.png
km_B_vax12_type_covidadmittedproxy1:
run: r:latest analysis/km.R B vax12_type covidadmittedproxy1
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/vax12_type/covidadmittedproxy1/*.txt
csv: output/match/B/km/vax12_type/covidadmittedproxy1/*.csv
png: output/match/B/km/vax12_type/covidadmittedproxy1/*.png
km_B_vax12_type_covidadmitted:
run: r:latest analysis/km.R B vax12_type covidadmitted
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/vax12_type/covidadmitted/*.txt
csv: output/match/B/km/vax12_type/covidadmitted/*.csv
png: output/match/B/km/vax12_type/covidadmitted/*.png
km_B_vax12_type_coviddeath:
run: r:latest analysis/km.R B vax12_type coviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/vax12_type/coviddeath/*.txt
csv: output/match/B/km/vax12_type/coviddeath/*.csv
png: output/match/B/km/vax12_type/coviddeath/*.png
km_B_vax12_type_noncoviddeath:
run: r:latest analysis/km.R B vax12_type noncoviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/vax12_type/noncoviddeath/*.txt
csv: output/match/B/km/vax12_type/noncoviddeath/*.csv
png: output/match/B/km/vax12_type/noncoviddeath/*.png
## ### Models by clinically vulnerable group (''cev_cv'')
km_B_cev_cv_postest:
run: r:latest analysis/km.R B cev_cv postest
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/cev_cv/postest/*.txt
csv: output/match/B/km/cev_cv/postest/*.csv
png: output/match/B/km/cev_cv/postest/*.png
km_B_cev_cv_covidemergency:
run: r:latest analysis/km.R B cev_cv covidemergency
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/cev_cv/covidemergency/*.txt
csv: output/match/B/km/cev_cv/covidemergency/*.csv
png: output/match/B/km/cev_cv/covidemergency/*.png
km_B_cev_cv_covidadmittedproxy1:
run: r:latest analysis/km.R B cev_cv covidadmittedproxy1
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/cev_cv/covidadmittedproxy1/*.txt
csv: output/match/B/km/cev_cv/covidadmittedproxy1/*.csv
png: output/match/B/km/cev_cv/covidadmittedproxy1/*.png
km_B_cev_cv_covidadmitted:
run: r:latest analysis/km.R B cev_cv covidadmitted
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/cev_cv/covidadmitted/*.txt
csv: output/match/B/km/cev_cv/covidadmitted/*.csv
png: output/match/B/km/cev_cv/covidadmitted/*.png
km_B_cev_cv_coviddeath:
run: r:latest analysis/km.R B cev_cv coviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/cev_cv/coviddeath/*.txt
csv: output/match/B/km/cev_cv/coviddeath/*.csv
png: output/match/B/km/cev_cv/coviddeath/*.png
km_B_cev_cv_noncoviddeath:
run: r:latest analysis/km.R B cev_cv noncoviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/cev_cv/noncoviddeath/*.txt
csv: output/match/B/km/cev_cv/noncoviddeath/*.csv
png: output/match/B/km/cev_cv/noncoviddeath/*.png
## ### Models by prior infection (''prior_covid_infection'')
km_B_prior_covid_infection_postest:
run: r:latest analysis/km.R B prior_covid_infection postest
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/prior_covid_infection/postest/*.txt
csv: output/match/B/km/prior_covid_infection/postest/*.csv
png: output/match/B/km/prior_covid_infection/postest/*.png
km_B_prior_covid_infection_covidemergency:
run: r:latest analysis/km.R B prior_covid_infection covidemergency
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/prior_covid_infection/covidemergency/*.txt
csv: output/match/B/km/prior_covid_infection/covidemergency/*.csv
png: output/match/B/km/prior_covid_infection/covidemergency/*.png
km_B_prior_covid_infection_covidadmittedproxy1:
run: r:latest analysis/km.R B prior_covid_infection covidadmittedproxy1
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/prior_covid_infection/covidadmittedproxy1/*.txt
csv: output/match/B/km/prior_covid_infection/covidadmittedproxy1/*.csv
png: output/match/B/km/prior_covid_infection/covidadmittedproxy1/*.png
km_B_prior_covid_infection_covidadmitted:
run: r:latest analysis/km.R B prior_covid_infection covidadmitted
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/prior_covid_infection/covidadmitted/*.txt
csv: output/match/B/km/prior_covid_infection/covidadmitted/*.csv
png: output/match/B/km/prior_covid_infection/covidadmitted/*.png
km_B_prior_covid_infection_coviddeath:
run: r:latest analysis/km.R B prior_covid_infection coviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/prior_covid_infection/coviddeath/*.txt
csv: output/match/B/km/prior_covid_infection/coviddeath/*.csv
png: output/match/B/km/prior_covid_infection/coviddeath/*.png
km_B_prior_covid_infection_noncoviddeath:
run: r:latest analysis/km.R B prior_covid_infection noncoviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/prior_covid_infection/noncoviddeath/*.txt
csv: output/match/B/km/prior_covid_infection/noncoviddeath/*.csv
png: output/match/B/km/prior_covid_infection/noncoviddeath/*.png
## ### Models by age (''age65plus'')
km_B_age65plus_postest:
run: r:latest analysis/km.R B age65plus postest
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/age65plus/postest/*.txt
csv: output/match/B/km/age65plus/postest/*.csv
png: output/match/B/km/age65plus/postest/*.png
km_B_age65plus_covidemergency:
run: r:latest analysis/km.R B age65plus covidemergency
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/age65plus/covidemergency/*.txt
csv: output/match/B/km/age65plus/covidemergency/*.csv
png: output/match/B/km/age65plus/covidemergency/*.png
km_B_age65plus_covidadmittedproxy1:
run: r:latest analysis/km.R B age65plus covidadmittedproxy1
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/age65plus/covidadmittedproxy1/*.txt
csv: output/match/B/km/age65plus/covidadmittedproxy1/*.csv
png: output/match/B/km/age65plus/covidadmittedproxy1/*.png
km_B_age65plus_covidadmitted:
run: r:latest analysis/km.R B age65plus covidadmitted
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/age65plus/covidadmitted/*.txt
csv: output/match/B/km/age65plus/covidadmitted/*.csv
png: output/match/B/km/age65plus/covidadmitted/*.png
km_B_age65plus_coviddeath:
run: r:latest analysis/km.R B age65plus coviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/age65plus/coviddeath/*.txt
csv: output/match/B/km/age65plus/coviddeath/*.csv
png: output/match/B/km/age65plus/coviddeath/*.png
km_B_age65plus_noncoviddeath:
run: r:latest analysis/km.R B age65plus noncoviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/age65plus/noncoviddeath/*.txt
csv: output/match/B/km/age65plus/noncoviddeath/*.csv
png: output/match/B/km/age65plus/noncoviddeath/*.png
## ### Models by variant era (''variantera'')
km_B_variantera_postest:
run: r:latest analysis/km.R B variantera postest
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/variantera/postest/*.txt
csv: output/match/B/km/variantera/postest/*.csv
png: output/match/B/km/variantera/postest/*.png
km_B_variantera_covidemergency:
run: r:latest analysis/km.R B variantera covidemergency
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/variantera/covidemergency/*.txt
csv: output/match/B/km/variantera/covidemergency/*.csv
png: output/match/B/km/variantera/covidemergency/*.png
km_B_variantera_covidadmittedproxy1:
run: r:latest analysis/km.R B variantera covidadmittedproxy1
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/variantera/covidadmittedproxy1/*.txt
csv: output/match/B/km/variantera/covidadmittedproxy1/*.csv
png: output/match/B/km/variantera/covidadmittedproxy1/*.png
km_B_variantera_covidadmitted:
run: r:latest analysis/km.R B variantera covidadmitted
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/variantera/covidadmitted/*.txt
csv: output/match/B/km/variantera/covidadmitted/*.csv
png: output/match/B/km/variantera/covidadmitted/*.png
km_B_variantera_coviddeath:
run: r:latest analysis/km.R B variantera coviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/variantera/coviddeath/*.txt
csv: output/match/B/km/variantera/coviddeath/*.csv
png: output/match/B/km/variantera/coviddeath/*.png
km_B_variantera_noncoviddeath:
run: r:latest analysis/km.R B variantera noncoviddeath
needs:
- match_B
- data_selection
outputs:
moderately_sensitive:
txt: output/match/B/km/variantera/noncoviddeath/*.txt
csv: output/match/B/km/variantera/noncoviddeath/*.csv
png: output/match/B/km/variantera/noncoviddeath/*.png
## # # # # # # # # # # # # # # # # # # #
## Combine KM estimates across outcomes and subgroups
## # # # # # # # # # # # # # # # # # # #
km_combine_A:
run: r:latest analysis/km_combine.R A
needs:
- km_A_all_postest
- km_A_all_covidemergency
- km_A_all_covidadmittedproxy1
- km_A_all_covidadmitted
- km_A_all_coviddeath
- km_A_all_noncoviddeath
- km_A_vax12_type_postest
- km_A_vax12_type_covidemergency
- km_A_vax12_type_covidadmittedproxy1
- km_A_vax12_type_covidadmitted
- km_A_vax12_type_coviddeath
- km_A_vax12_type_noncoviddeath
- km_A_prior_covid_infection_postest
- km_A_prior_covid_infection_covidemergency
- km_A_prior_covid_infection_covidadmittedproxy1
- km_A_prior_covid_infection_covidadmitted
- km_A_prior_covid_infection_coviddeath
- km_A_prior_covid_infection_noncoviddeath
- km_A_age65plus_postest
- km_A_age65plus_covidemergency
- km_A_age65plus_covidadmittedproxy1
- km_A_age65plus_covidadmitted
- km_A_age65plus_coviddeath
- km_A_age65plus_noncoviddeath
- km_A_cev_cv_postest
- km_A_cev_cv_covidemergency
- km_A_cev_cv_covidadmittedproxy1
- km_A_cev_cv_covidadmitted
- km_A_cev_cv_coviddeath
- km_A_cev_cv_noncoviddeath
- km_A_variantera_postest
- km_A_variantera_covidemergency
- km_A_variantera_covidadmittedproxy1
- km_A_variantera_covidadmitted
- km_A_variantera_coviddeath
- km_A_variantera_noncoviddeath
outputs:
moderately_sensitive:
csv: output/match/A/km/combined/*.csv
png: output/match/A/km/combined/plots/*.png
km_combine_B:
run: r:latest analysis/km_combine.R B
needs:
- km_B_all_postest
- km_B_all_covidemergency
- km_B_all_covidadmittedproxy1
- km_B_all_covidadmitted
- km_B_all_coviddeath
- km_B_all_noncoviddeath
- km_B_vax12_type_postest