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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: ehrql:v0 generate-dataset analysis/dataset_definition.py --output output/extracts/extract.arrow
--dummy-data-file analysis/dummydata/dummyextract.arrow
needs: []
outputs:
highly_sensitive:
arrow: output/extracts/extract.arrow
data_process:
run: r:latest analysis/data_process.R
needs:
- extract
outputs:
highly_sensitive:
rds: output/data/*.rds
data_skim:
run: r:latest analysis/data_skim.R output/data/data_processed.rds output/data/skim
needs:
- data_process
outputs:
moderately_sensitive:
cohort: output/data/skim/*.txt
geography:
run: r:latest analysis/geography.R
needs:
- data_process
outputs:
moderately_sensitive:
png: output/geography/*.png
csv: output/geography/*.csv
## # # # # # # # # # # # # # # # # # # #
## Cohort: age75plus
## # # # # # # # # # # # # # # # # # # #
data_selection_age75plus:
run: r:latest analysis/data_selection.R age75plus
needs:
- data_process
outputs:
highly_sensitive:
rds: output/age75plus/*.rds
moderately_sensitive:
csv: output/age75plus/*.csv
skim_selection_age75plus:
run: r:latest analysis/data_skim.R output/age75plus/data_cohort.rds output/age75plus/skim
needs:
- data_selection_age75plus
outputs:
moderately_sensitive:
txt: output/age75plus/skim/*.txt
## # # # # # # # # # # # # # # # # # # #
## matching set A
## # # # # # # # # # # # # # # # # # # #
match_age75plus_A:
run: r:latest analysis/match.R age75plus A
needs:
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/*.rds
match_report_age75plus_A:
run: r:latest analysis/match_report.R age75plus A
needs:
- data_selection_age75plus
- match_age75plus_A
outputs:
moderately_sensitive:
csv: output/age75plus/A/report/*.csv
png: output/age75plus/A/report/*.png
## ### Overall models (''all'')
km_age75plus_A_all_covidemergency:
run: r:latest analysis/km.R age75plus A all covidemergency
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/all/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/A/km/all/covidemergency/*.png
km_age75plus_A_all_covidadmitted:
run: r:latest analysis/km.R age75plus A all covidadmitted
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/all/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/A/km/all/covidadmitted/*.png
km_age75plus_A_all_covidcritcare:
run: r:latest analysis/km.R age75plus A all covidcritcare
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/all/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/A/km/all/covidcritcare/*.png
km_age75plus_A_all_coviddeath:
run: r:latest analysis/km.R age75plus A all coviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/all/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/all/coviddeath/*.png
km_age75plus_A_all_noncoviddeath:
run: r:latest analysis/km.R age75plus A all noncoviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/all/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/all/noncoviddeath/*.png
km_age75plus_A_all_fracture:
run: r:latest analysis/km.R age75plus A all fracture
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/all/fracture/*.rds
moderately_sensitive:
png: output/age75plus/A/km/all/fracture/*.png
## ### Models by age-band (''ageband'')
km_age75plus_A_ageband_covidemergency:
run: r:latest analysis/km.R age75plus A ageband covidemergency
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/ageband/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/A/km/ageband/covidemergency/*.png
km_age75plus_A_ageband_covidadmitted:
run: r:latest analysis/km.R age75plus A ageband covidadmitted
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/ageband/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/A/km/ageband/covidadmitted/*.png
km_age75plus_A_ageband_covidcritcare:
run: r:latest analysis/km.R age75plus A ageband covidcritcare
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/ageband/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/A/km/ageband/covidcritcare/*.png
km_age75plus_A_ageband_coviddeath:
run: r:latest analysis/km.R age75plus A ageband coviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/ageband/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/ageband/coviddeath/*.png
km_age75plus_A_ageband_noncoviddeath:
run: r:latest analysis/km.R age75plus A ageband noncoviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/ageband/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/ageband/noncoviddeath/*.png
km_age75plus_A_ageband_fracture:
run: r:latest analysis/km.R age75plus A ageband fracture
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/ageband/fracture/*.rds
moderately_sensitive:
png: output/age75plus/A/km/ageband/fracture/*.png
## ### Models by clinically vulnerable group (''cv'')
km_age75plus_A_cv_covidemergency:
run: r:latest analysis/km.R age75plus A cv covidemergency
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/cv/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/A/km/cv/covidemergency/*.png
km_age75plus_A_cv_covidadmitted:
run: r:latest analysis/km.R age75plus A cv covidadmitted
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/cv/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/A/km/cv/covidadmitted/*.png
km_age75plus_A_cv_covidcritcare:
run: r:latest analysis/km.R age75plus A cv covidcritcare
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/cv/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/A/km/cv/covidcritcare/*.png
km_age75plus_A_cv_coviddeath:
run: r:latest analysis/km.R age75plus A cv coviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/cv/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/cv/coviddeath/*.png
km_age75plus_A_cv_noncoviddeath:
run: r:latest analysis/km.R age75plus A cv noncoviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/cv/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/cv/noncoviddeath/*.png
km_age75plus_A_cv_fracture:
run: r:latest analysis/km.R age75plus A cv fracture
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/cv/fracture/*.rds
moderately_sensitive:
png: output/age75plus/A/km/cv/fracture/*.png
## ### Models by prior infection (''prior_covid_infection'')
km_age75plus_A_prior_covid_infection_covidemergency:
run: r:latest analysis/km.R age75plus A prior_covid_infection covidemergency
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/prior_covid_infection/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/A/km/prior_covid_infection/covidemergency/*.png
km_age75plus_A_prior_covid_infection_covidadmitted:
run: r:latest analysis/km.R age75plus A prior_covid_infection covidadmitted
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/prior_covid_infection/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/A/km/prior_covid_infection/covidadmitted/*.png
km_age75plus_A_prior_covid_infection_covidcritcare:
run: r:latest analysis/km.R age75plus A prior_covid_infection covidcritcare
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/prior_covid_infection/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/A/km/prior_covid_infection/covidcritcare/*.png
km_age75plus_A_prior_covid_infection_coviddeath:
run: r:latest analysis/km.R age75plus A prior_covid_infection coviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/prior_covid_infection/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/prior_covid_infection/coviddeath/*.png
km_age75plus_A_prior_covid_infection_noncoviddeath:
run: r:latest analysis/km.R age75plus A prior_covid_infection noncoviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/prior_covid_infection/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/prior_covid_infection/noncoviddeath/*.png
km_age75plus_A_prior_covid_infection_fracture:
run: r:latest analysis/km.R age75plus A prior_covid_infection fracture
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/prior_covid_infection/fracture/*.rds
moderately_sensitive:
png: output/age75plus/A/km/prior_covid_infection/fracture/*.png
## ### Models by vax history (''vax_previous_count'')
km_age75plus_A_vax_previous_count_covidemergency:
run: r:latest analysis/km.R age75plus A vax_previous_count covidemergency
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/vax_previous_count/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/A/km/vax_previous_count/covidemergency/*.png
km_age75plus_A_vax_previous_count_covidadmitted:
run: r:latest analysis/km.R age75plus A vax_previous_count covidadmitted
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/vax_previous_count/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/A/km/vax_previous_count/covidadmitted/*.png
km_age75plus_A_vax_previous_count_covidcritcare:
run: r:latest analysis/km.R age75plus A vax_previous_count covidcritcare
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/vax_previous_count/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/A/km/vax_previous_count/covidcritcare/*.png
km_age75plus_A_vax_previous_count_coviddeath:
run: r:latest analysis/km.R age75plus A vax_previous_count coviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/vax_previous_count/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/vax_previous_count/coviddeath/*.png
km_age75plus_A_vax_previous_count_noncoviddeath:
run: r:latest analysis/km.R age75plus A vax_previous_count noncoviddeath
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/vax_previous_count/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/A/km/vax_previous_count/noncoviddeath/*.png
km_age75plus_A_vax_previous_count_fracture:
run: r:latest analysis/km.R age75plus A vax_previous_count fracture
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/km/vax_previous_count/fracture/*.rds
moderately_sensitive:
png: output/age75plus/A/km/vax_previous_count/fracture/*.png
eventcounts_age75plus_A:
run: r:latest analysis/eventcounts.R age75plus A
needs:
- match_age75plus_A
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/A/eventcounts/*.rds
## # # # # # # # # # # # # # # # # # # #
## matching set B
## # # # # # # # # # # # # # # # # # # #
match_age75plus_B:
run: r:latest analysis/match.R age75plus B
needs:
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/*.rds
match_report_age75plus_B:
run: r:latest analysis/match_report.R age75plus B
needs:
- data_selection_age75plus
- match_age75plus_B
outputs:
moderately_sensitive:
csv: output/age75plus/B/report/*.csv
png: output/age75plus/B/report/*.png
## ### Overall models (''all'')
km_age75plus_B_all_covidemergency:
run: r:latest analysis/km.R age75plus B all covidemergency
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/all/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/B/km/all/covidemergency/*.png
km_age75plus_B_all_covidadmitted:
run: r:latest analysis/km.R age75plus B all covidadmitted
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/all/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/B/km/all/covidadmitted/*.png
km_age75plus_B_all_covidcritcare:
run: r:latest analysis/km.R age75plus B all covidcritcare
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/all/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/B/km/all/covidcritcare/*.png
km_age75plus_B_all_coviddeath:
run: r:latest analysis/km.R age75plus B all coviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/all/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/all/coviddeath/*.png
km_age75plus_B_all_noncoviddeath:
run: r:latest analysis/km.R age75plus B all noncoviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/all/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/all/noncoviddeath/*.png
km_age75plus_B_all_fracture:
run: r:latest analysis/km.R age75plus B all fracture
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/all/fracture/*.rds
moderately_sensitive:
png: output/age75plus/B/km/all/fracture/*.png
## ### Models by age-band (''ageband'')
km_age75plus_B_ageband_covidemergency:
run: r:latest analysis/km.R age75plus B ageband covidemergency
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/ageband/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/B/km/ageband/covidemergency/*.png
km_age75plus_B_ageband_covidadmitted:
run: r:latest analysis/km.R age75plus B ageband covidadmitted
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/ageband/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/B/km/ageband/covidadmitted/*.png
km_age75plus_B_ageband_covidcritcare:
run: r:latest analysis/km.R age75plus B ageband covidcritcare
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/ageband/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/B/km/ageband/covidcritcare/*.png
km_age75plus_B_ageband_coviddeath:
run: r:latest analysis/km.R age75plus B ageband coviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/ageband/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/ageband/coviddeath/*.png
km_age75plus_B_ageband_noncoviddeath:
run: r:latest analysis/km.R age75plus B ageband noncoviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/ageband/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/ageband/noncoviddeath/*.png
km_age75plus_B_ageband_fracture:
run: r:latest analysis/km.R age75plus B ageband fracture
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/ageband/fracture/*.rds
moderately_sensitive:
png: output/age75plus/B/km/ageband/fracture/*.png
## ### Models by clinically vulnerable group (''cv'')
km_age75plus_B_cv_covidemergency:
run: r:latest analysis/km.R age75plus B cv covidemergency
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/cv/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/B/km/cv/covidemergency/*.png
km_age75plus_B_cv_covidadmitted:
run: r:latest analysis/km.R age75plus B cv covidadmitted
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/cv/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/B/km/cv/covidadmitted/*.png
km_age75plus_B_cv_covidcritcare:
run: r:latest analysis/km.R age75plus B cv covidcritcare
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/cv/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/B/km/cv/covidcritcare/*.png
km_age75plus_B_cv_coviddeath:
run: r:latest analysis/km.R age75plus B cv coviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/cv/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/cv/coviddeath/*.png
km_age75plus_B_cv_noncoviddeath:
run: r:latest analysis/km.R age75plus B cv noncoviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/cv/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/cv/noncoviddeath/*.png
km_age75plus_B_cv_fracture:
run: r:latest analysis/km.R age75plus B cv fracture
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/cv/fracture/*.rds
moderately_sensitive:
png: output/age75plus/B/km/cv/fracture/*.png
## ### Models by vax history (''vax_previous_count'')
km_age75plus_B_vax_previous_count_covidemergency:
run: r:latest analysis/km.R age75plus B vax_previous_count covidemergency
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/vax_previous_count/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/B/km/vax_previous_count/covidemergency/*.png
km_age75plus_B_vax_previous_count_covidadmitted:
run: r:latest analysis/km.R age75plus B vax_previous_count covidadmitted
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/vax_previous_count/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/B/km/vax_previous_count/covidadmitted/*.png
km_age75plus_B_vax_previous_count_covidcritcare:
run: r:latest analysis/km.R age75plus B vax_previous_count covidcritcare
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/vax_previous_count/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/B/km/vax_previous_count/covidcritcare/*.png
km_age75plus_B_vax_previous_count_coviddeath:
run: r:latest analysis/km.R age75plus B vax_previous_count coviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/vax_previous_count/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/vax_previous_count/coviddeath/*.png
km_age75plus_B_vax_previous_count_noncoviddeath:
run: r:latest analysis/km.R age75plus B vax_previous_count noncoviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/vax_previous_count/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/vax_previous_count/noncoviddeath/*.png
km_age75plus_B_vax_previous_count_fracture:
run: r:latest analysis/km.R age75plus B vax_previous_count fracture
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/vax_previous_count/fracture/*.rds
moderately_sensitive:
png: output/age75plus/B/km/vax_previous_count/fracture/*.png
## ### Models by prior infection (''prior_covid_infection'')
km_age75plus_B_prior_covid_infection_covidemergency:
run: r:latest analysis/km.R age75plus B prior_covid_infection covidemergency
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/prior_covid_infection/covidemergency/*.rds
moderately_sensitive:
png: output/age75plus/B/km/prior_covid_infection/covidemergency/*.png
km_age75plus_B_prior_covid_infection_covidadmitted:
run: r:latest analysis/km.R age75plus B prior_covid_infection covidadmitted
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/prior_covid_infection/covidadmitted/*.rds
moderately_sensitive:
png: output/age75plus/B/km/prior_covid_infection/covidadmitted/*.png
km_age75plus_B_prior_covid_infection_covidcritcare:
run: r:latest analysis/km.R age75plus B prior_covid_infection covidcritcare
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/prior_covid_infection/covidcritcare/*.rds
moderately_sensitive:
png: output/age75plus/B/km/prior_covid_infection/covidcritcare/*.png
km_age75plus_B_prior_covid_infection_coviddeath:
run: r:latest analysis/km.R age75plus B prior_covid_infection coviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/prior_covid_infection/coviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/prior_covid_infection/coviddeath/*.png
km_age75plus_B_prior_covid_infection_noncoviddeath:
run: r:latest analysis/km.R age75plus B prior_covid_infection noncoviddeath
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/prior_covid_infection/noncoviddeath/*.rds
moderately_sensitive:
png: output/age75plus/B/km/prior_covid_infection/noncoviddeath/*.png
km_age75plus_B_prior_covid_infection_fracture:
run: r:latest analysis/km.R age75plus B prior_covid_infection fracture
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/km/prior_covid_infection/fracture/*.rds
moderately_sensitive:
png: output/age75plus/B/km/prior_covid_infection/fracture/*.png
eventcounts_age75plus_B:
run: r:latest analysis/eventcounts.R age75plus B
needs:
- match_age75plus_B
- data_selection_age75plus
outputs:
highly_sensitive:
rds: output/age75plus/B/eventcounts/*.rds
## # # # # # # # # # # # # # # # # # # #
## Cohort: cv
## # # # # # # # # # # # # # # # # # # #
data_selection_cv:
run: r:latest analysis/data_selection.R cv
needs:
- data_process
outputs:
highly_sensitive:
rds: output/cv/*.rds
moderately_sensitive:
csv: output/cv/*.csv
skim_selection_cv:
run: r:latest analysis/data_skim.R output/cv/data_cohort.rds output/cv/skim
needs:
- data_selection_cv
outputs:
moderately_sensitive:
txt: output/cv/skim/*.txt
## # # # # # # # # # # # # # # # # # # #
## matching set A
## # # # # # # # # # # # # # # # # # # #
match_cv_A:
run: r:latest analysis/match.R cv A
needs:
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/*.rds
match_report_cv_A:
run: r:latest analysis/match_report.R cv A
needs:
- data_selection_cv
- match_cv_A
outputs:
moderately_sensitive:
csv: output/cv/A/report/*.csv
png: output/cv/A/report/*.png
## ### Overall models (''all'')
km_cv_A_all_covidemergency:
run: r:latest analysis/km.R cv A all covidemergency
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/all/covidemergency/*.rds
moderately_sensitive:
png: output/cv/A/km/all/covidemergency/*.png
km_cv_A_all_covidadmitted:
run: r:latest analysis/km.R cv A all covidadmitted
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/all/covidadmitted/*.rds
moderately_sensitive:
png: output/cv/A/km/all/covidadmitted/*.png
km_cv_A_all_covidcritcare:
run: r:latest analysis/km.R cv A all covidcritcare
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/all/covidcritcare/*.rds
moderately_sensitive:
png: output/cv/A/km/all/covidcritcare/*.png
km_cv_A_all_coviddeath:
run: r:latest analysis/km.R cv A all coviddeath
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/all/coviddeath/*.rds
moderately_sensitive:
png: output/cv/A/km/all/coviddeath/*.png
km_cv_A_all_noncoviddeath:
run: r:latest analysis/km.R cv A all noncoviddeath
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/all/noncoviddeath/*.rds
moderately_sensitive:
png: output/cv/A/km/all/noncoviddeath/*.png
km_cv_A_all_fracture:
run: r:latest analysis/km.R cv A all fracture
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/all/fracture/*.rds
moderately_sensitive:
png: output/cv/A/km/all/fracture/*.png
## ### Models by age-band (''ageband'')
km_cv_A_ageband_covidemergency:
run: r:latest analysis/km.R cv A ageband covidemergency
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/ageband/covidemergency/*.rds
moderately_sensitive:
png: output/cv/A/km/ageband/covidemergency/*.png
km_cv_A_ageband_covidadmitted:
run: r:latest analysis/km.R cv A ageband covidadmitted
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/ageband/covidadmitted/*.rds
moderately_sensitive:
png: output/cv/A/km/ageband/covidadmitted/*.png
km_cv_A_ageband_covidcritcare:
run: r:latest analysis/km.R cv A ageband covidcritcare
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/ageband/covidcritcare/*.rds
moderately_sensitive:
png: output/cv/A/km/ageband/covidcritcare/*.png
km_cv_A_ageband_coviddeath:
run: r:latest analysis/km.R cv A ageband coviddeath
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/ageband/coviddeath/*.rds
moderately_sensitive:
png: output/cv/A/km/ageband/coviddeath/*.png
km_cv_A_ageband_noncoviddeath:
run: r:latest analysis/km.R cv A ageband noncoviddeath
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/ageband/noncoviddeath/*.rds
moderately_sensitive:
png: output/cv/A/km/ageband/noncoviddeath/*.png
km_cv_A_ageband_fracture:
run: r:latest analysis/km.R cv A ageband fracture
needs:
- match_cv_A
- data_selection_cv
outputs:
highly_sensitive:
rds: output/cv/A/km/ageband/fracture/*.rds
moderately_sensitive:
png: output/cv/A/km/ageband/fracture/*.png
## ### Models by prior infection (''prior_covid_infection'')
km_cv_A_prior_covid_infection_covidemergency: