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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 100000
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
## # # # # # # # # # # # # # # # # # # #
##
## # # # # # # # # # # # # # # # # # # #
## Vax1, Over 12s cohort
## # # # # # # # # # # # # # # # # # # #
## # # # # # # # # # # # # # # # # # # #
## Extract and match
extract_treated_over12_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_treated
--output-file output/over12/vax1/extract/input_treated.feather --param cohort=over12
--param vaxn=1
outputs:
highly_sensitive:
extract: output/over12/vax1/extract/input_treated.feather
process_treated_over12_1:
run: r:latest analysis/treated/process_treated.R over12 1
needs:
- extract_treated_over12_1
outputs:
highly_sensitive:
rds: output/over12/vax1/treated/*.rds
extract_controlpotential_over12_1_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax1/matchround1/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=1 --param index_date=2021-09-20
--param vaxn=1
needs: []
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround1/extract/input_controlpotential.feather
process_controlpotential_over12_1_1:
run: r:latest analysis/matching/process_controlpotential.R over12 1 1
needs:
- extract_controlpotential_over12_1_1
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround1/process/*.rds
match_potential_over12_1_1:
run: r:latest analysis/matching/match_potential.R over12 1 1
needs:
- process_treated_over12_1
- process_controlpotential_over12_1_1
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround1/potential/*.rds
csv: output/over12/vax1/matchround1/potential/*.csv.gz
extract_controlactual_over12_1_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax1/matchround1/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=1 --param vaxn=1
needs:
- match_potential_over12_1_1
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround1/extract/input_controlactual.feather
process_controlactual_over12_1_1:
run: r:latest analysis/matching/process_controlactual.R over12 1 1
needs:
- process_treated_over12_1
- match_potential_over12_1_1
- extract_controlpotential_over12_1_1
- extract_controlactual_over12_1_1
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround1/actual/*.rds
csv: output/over12/vax1/matchround1/actual/*.csv.gz
extract_controlpotential_over12_1_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax1/matchround2/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=2 --param index_date=2021-10-04
--param vaxn=1
needs:
- process_controlactual_over12_1_1
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround2/extract/input_controlpotential.feather
process_controlpotential_over12_1_2:
run: r:latest analysis/matching/process_controlpotential.R over12 1 2
needs:
- extract_controlpotential_over12_1_2
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround2/process/*.rds
match_potential_over12_1_2:
run: r:latest analysis/matching/match_potential.R over12 1 2
needs:
- process_treated_over12_1
- process_controlpotential_over12_1_2
- process_controlactual_over12_1_1
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround2/potential/*.rds
csv: output/over12/vax1/matchround2/potential/*.csv.gz
extract_controlactual_over12_1_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax1/matchround2/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=2 --param vaxn=1
needs:
- match_potential_over12_1_2
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround2/extract/input_controlactual.feather
process_controlactual_over12_1_2:
run: r:latest analysis/matching/process_controlactual.R over12 1 2
needs:
- process_treated_over12_1
- match_potential_over12_1_2
- extract_controlpotential_over12_1_2
- extract_controlactual_over12_1_2
- process_controlactual_over12_1_1
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround2/actual/*.rds
csv: output/over12/vax1/matchround2/actual/*.csv.gz
extract_controlpotential_over12_1_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax1/matchround3/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=3 --param index_date=2021-10-18
--param vaxn=1
needs:
- process_controlactual_over12_1_2
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround3/extract/input_controlpotential.feather
process_controlpotential_over12_1_3:
run: r:latest analysis/matching/process_controlpotential.R over12 1 3
needs:
- extract_controlpotential_over12_1_3
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround3/process/*.rds
match_potential_over12_1_3:
run: r:latest analysis/matching/match_potential.R over12 1 3
needs:
- process_treated_over12_1
- process_controlpotential_over12_1_3
- process_controlactual_over12_1_2
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround3/potential/*.rds
csv: output/over12/vax1/matchround3/potential/*.csv.gz
extract_controlactual_over12_1_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax1/matchround3/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=3 --param vaxn=1
needs:
- match_potential_over12_1_3
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround3/extract/input_controlactual.feather
process_controlactual_over12_1_3:
run: r:latest analysis/matching/process_controlactual.R over12 1 3
needs:
- process_treated_over12_1
- match_potential_over12_1_3
- extract_controlpotential_over12_1_3
- extract_controlactual_over12_1_3
- process_controlactual_over12_1_2
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround3/actual/*.rds
csv: output/over12/vax1/matchround3/actual/*.csv.gz
extract_controlpotential_over12_1_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax1/matchround4/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=4 --param index_date=2021-11-01
--param vaxn=1
needs:
- process_controlactual_over12_1_3
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround4/extract/input_controlpotential.feather
process_controlpotential_over12_1_4:
run: r:latest analysis/matching/process_controlpotential.R over12 1 4
needs:
- extract_controlpotential_over12_1_4
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround4/process/*.rds
match_potential_over12_1_4:
run: r:latest analysis/matching/match_potential.R over12 1 4
needs:
- process_treated_over12_1
- process_controlpotential_over12_1_4
- process_controlactual_over12_1_3
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround4/potential/*.rds
csv: output/over12/vax1/matchround4/potential/*.csv.gz
extract_controlactual_over12_1_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax1/matchround4/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=4 --param vaxn=1
needs:
- match_potential_over12_1_4
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround4/extract/input_controlactual.feather
process_controlactual_over12_1_4:
run: r:latest analysis/matching/process_controlactual.R over12 1 4
needs:
- process_treated_over12_1
- match_potential_over12_1_4
- extract_controlpotential_over12_1_4
- extract_controlactual_over12_1_4
- process_controlactual_over12_1_3
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround4/actual/*.rds
csv: output/over12/vax1/matchround4/actual/*.csv.gz
extract_controlpotential_over12_1_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax1/matchround5/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=5 --param index_date=2021-11-15
--param vaxn=1
needs:
- process_controlactual_over12_1_4
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround5/extract/input_controlpotential.feather
process_controlpotential_over12_1_5:
run: r:latest analysis/matching/process_controlpotential.R over12 1 5
needs:
- extract_controlpotential_over12_1_5
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround5/process/*.rds
match_potential_over12_1_5:
run: r:latest analysis/matching/match_potential.R over12 1 5
needs:
- process_treated_over12_1
- process_controlpotential_over12_1_5
- process_controlactual_over12_1_4
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround5/potential/*.rds
csv: output/over12/vax1/matchround5/potential/*.csv.gz
extract_controlactual_over12_1_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax1/matchround5/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=5 --param vaxn=1
needs:
- match_potential_over12_1_5
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround5/extract/input_controlactual.feather
process_controlactual_over12_1_5:
run: r:latest analysis/matching/process_controlactual.R over12 1 5
needs:
- process_treated_over12_1
- match_potential_over12_1_5
- extract_controlpotential_over12_1_5
- extract_controlactual_over12_1_5
- process_controlactual_over12_1_4
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround5/actual/*.rds
csv: output/over12/vax1/matchround5/actual/*.csv.gz
extract_controlpotential_over12_1_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax1/matchround6/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=6 --param index_date=2021-11-29
--param vaxn=1
needs:
- process_controlactual_over12_1_5
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround6/extract/input_controlpotential.feather
process_controlpotential_over12_1_6:
run: r:latest analysis/matching/process_controlpotential.R over12 1 6
needs:
- extract_controlpotential_over12_1_6
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround6/process/*.rds
match_potential_over12_1_6:
run: r:latest analysis/matching/match_potential.R over12 1 6
needs:
- process_treated_over12_1
- process_controlpotential_over12_1_6
- process_controlactual_over12_1_5
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround6/potential/*.rds
csv: output/over12/vax1/matchround6/potential/*.csv.gz
extract_controlactual_over12_1_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax1/matchround6/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=6 --param vaxn=1
needs:
- match_potential_over12_1_6
outputs:
highly_sensitive:
cohort: output/over12/vax1/matchround6/extract/input_controlactual.feather
process_controlactual_over12_1_6:
run: r:latest analysis/matching/process_controlactual.R over12 1 6
needs:
- process_treated_over12_1
- match_potential_over12_1_6
- extract_controlpotential_over12_1_6
- extract_controlactual_over12_1_6
- process_controlactual_over12_1_5
outputs:
highly_sensitive:
rds: output/over12/vax1/matchround6/actual/*.rds
csv: output/over12/vax1/matchround6/actual/*.csv.gz
extract_controlfinal_over12_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlfinal
--output-file output/over12/vax1/extract/input_controlfinal.feather --param
cohort=over12 --param n_matching_rounds=6 --param vaxn=1
needs:
- process_controlactual_over12_1_6
outputs:
highly_sensitive:
extract: output/over12/vax1/extract/input_controlfinal.feather
process_controlfinal_over12_1:
run: r:latest analysis/matching/process_controlfinal.R over12 1
needs:
- process_controlactual_over12_1_1
- process_controlactual_over12_1_2
- process_controlactual_over12_1_3
- process_controlactual_over12_1_4
- process_controlactual_over12_1_5
- process_controlactual_over12_1_6
- extract_controlfinal_over12_1
- process_treated_over12_1
outputs:
highly_sensitive:
extract: output/over12/vax1/match/*.rds
extract_csv: output/over12/vax1/match/*.csv.gz
skim_over12_1_treated:
run: r:latest analysis/data_skim.R output/over12/vax1/treated/data_treatedeligible.rds
output/over12/vax1/skim/treated
needs:
- process_treated_over12_1
outputs:
moderately_sensitive:
cohort: output/over12/vax1/skim/treated/*.txt
skim_over12_1_control:
run: r:latest analysis/data_skim.R output/over12/vax1/matchround1/process/data_controlpotential.rds
output/over12/vax1/skim/control
needs:
- process_controlpotential_over12_1_1
outputs:
moderately_sensitive:
cohort: output/over12/vax1/skim/control/*.txt
skim_over12_1_matched:
run: r:latest analysis/data_skim.R output/over12/vax1/match/data_matched.rds output/over12/vax1/skim
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
cohort: output/over12/vax1/skim/*.txt
table1_over12_1:
run: r:latest analysis/matching/table1.R over12 1
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
csv: output/over12/vax1/table1/*.csv
## # # # # # # # # # # # # # # # # # # #
## Model
km_over12_1_all_postest:
run: r:latest analysis/model/km.R over12 1 all postest
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/postest/*.rds
png: output/over12/vax1/models/km/all/postest/*.png
km_over12_1_all_emergency:
run: r:latest analysis/model/km.R over12 1 all emergency
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/emergency/*.rds
png: output/over12/vax1/models/km/all/emergency/*.png
km_over12_1_all_covidemergency:
run: r:latest analysis/model/km.R over12 1 all covidemergency
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/covidemergency/*.rds
png: output/over12/vax1/models/km/all/covidemergency/*.png
km_over12_1_all_covidadmitted:
run: r:latest analysis/model/km.R over12 1 all covidadmitted
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/covidadmitted/*.rds
png: output/over12/vax1/models/km/all/covidadmitted/*.png
km_over12_1_all_covidcritcare:
run: r:latest analysis/model/km.R over12 1 all covidcritcare
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/covidcritcare/*.rds
png: output/over12/vax1/models/km/all/covidcritcare/*.png
km_over12_1_all_coviddeath:
run: r:latest analysis/model/km.R over12 1 all coviddeath
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/coviddeath/*.rds
png: output/over12/vax1/models/km/all/coviddeath/*.png
km_over12_1_all_noncoviddeath:
run: r:latest analysis/model/km.R over12 1 all noncoviddeath
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/noncoviddeath/*.rds
png: output/over12/vax1/models/km/all/noncoviddeath/*.png
km_over12_1_all_admitted_unplanned:
run: r:latest analysis/model/km.R over12 1 all admitted_unplanned
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/admitted_unplanned/*.rds
png: output/over12/vax1/models/km/all/admitted_unplanned/*.png
km_over12_1_all_pericarditis:
run: r:latest analysis/model/km.R over12 1 all pericarditis
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/pericarditis/*.rds
png: output/over12/vax1/models/km/all/pericarditis/*.png
km_over12_1_all_myocarditis:
run: r:latest analysis/model/km.R over12 1 all myocarditis
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/myocarditis/*.rds
png: output/over12/vax1/models/km/all/myocarditis/*.png
km_over12_1_all_fracture:
run: r:latest analysis/model/km.R over12 1 all fracture
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/fracture/*.rds
png: output/over12/vax1/models/km/all/fracture/*.png
km_over12_1_all_noncovidadmitted:
run: r:latest analysis/model/km.R over12 1 all noncovidadmitted
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/noncovidadmitted/*.rds
png: output/over12/vax1/models/km/all/noncovidadmitted/*.png
km_over12_1_all_outcome_vax_2:
run: r:latest analysis/model/km.R over12 1 all outcome_vax_2
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/all/outcome_vax_2/*.rds
png: output/over12/vax1/models/km/all/outcome_vax_2/*.png
km_over12_1_prior_covid_infection_postest:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection postest
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/postest/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/postest/*.png
km_over12_1_prior_covid_infection_emergency:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection emergency
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/emergency/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/emergency/*.png
km_over12_1_prior_covid_infection_covidemergency:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection covidemergency
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/covidemergency/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/covidemergency/*.png
km_over12_1_prior_covid_infection_covidadmitted:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection covidadmitted
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/covidadmitted/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/covidadmitted/*.png
km_over12_1_prior_covid_infection_covidcritcare:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection covidcritcare
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/covidcritcare/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/covidcritcare/*.png
km_over12_1_prior_covid_infection_coviddeath:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection coviddeath
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/coviddeath/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/coviddeath/*.png
km_over12_1_prior_covid_infection_noncoviddeath:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection noncoviddeath
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/noncoviddeath/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/noncoviddeath/*.png
km_over12_1_prior_covid_infection_admitted_unplanned:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection admitted_unplanned
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/admitted_unplanned/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/admitted_unplanned/*.png
km_over12_1_prior_covid_infection_pericarditis:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection pericarditis
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/pericarditis/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/pericarditis/*.png
km_over12_1_prior_covid_infection_myocarditis:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection myocarditis
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/myocarditis/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/myocarditis/*.png
km_over12_1_prior_covid_infection_fracture:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection fracture
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/fracture/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/fracture/*.png
km_over12_1_prior_covid_infection_outcome_vax_2:
run: r:latest analysis/model/km.R over12 1 prior_covid_infection outcome_vax_2
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/km/prior_covid_infection/outcome_vax_2/*.rds
png: output/over12/vax1/models/km/prior_covid_infection/outcome_vax_2/*.png
eventcounts_over12_1_all:
run: r:latest analysis/model/eventcounts.R over12 1 all
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/eventcounts/all/*.rds
eventcounts_over12_1_prior_covid_infection:
run: r:latest analysis/model/eventcounts.R over12 1 prior_covid_infection
needs:
- process_controlfinal_over12_1
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/eventcounts/prior_covid_infection/*.rds
combine_over12_1:
run: r:latest analysis/model/combine.R over12 1
needs:
- km_over12_1_all_postest
- km_over12_1_all_emergency
- km_over12_1_all_covidemergency
- km_over12_1_all_covidadmitted
- km_over12_1_all_covidcritcare
- km_over12_1_all_coviddeath
- km_over12_1_all_noncoviddeath
- km_over12_1_all_admitted_unplanned
- km_over12_1_all_pericarditis
- km_over12_1_all_myocarditis
- km_over12_1_all_fracture
- km_over12_1_all_outcome_vax_2
- km_over12_1_prior_covid_infection_postest
- km_over12_1_prior_covid_infection_emergency
- km_over12_1_prior_covid_infection_covidemergency
- km_over12_1_prior_covid_infection_covidadmitted
- km_over12_1_prior_covid_infection_covidcritcare
- km_over12_1_prior_covid_infection_coviddeath
- km_over12_1_prior_covid_infection_noncoviddeath
- km_over12_1_prior_covid_infection_admitted_unplanned
- km_over12_1_prior_covid_infection_pericarditis
- km_over12_1_prior_covid_infection_myocarditis
- km_over12_1_prior_covid_infection_fracture
- km_over12_1_prior_covid_infection_outcome_vax_2
- eventcounts_over12_1_all
- eventcounts_over12_1_prior_covid_infection
outputs:
moderately_sensitive:
rds: output/over12/vax1/models/combined/*.csv
png: output/over12/vax1/models/combined/*.png
carditis_over12_1:
run: r:latest analysis/carditis.R over12 1 all
needs:
- process_controlfinal_over12_1
outputs:
highly_sensitive:
extract: output/over12/vax1/carditis_severity/*_dates.csv
moderately_sensitive:
csv: output/over12/vax1/carditis_severity/*_severity.csv
extract_carditis_date_over12_1_myo:
run: cohortextractor:latest generate_cohort --study-definition study_definition_carditis_severity
--output-file output/over12/vax1/extract/input_myocarditis_severity.feather
--param cohort=over12 --param vaxn=1 --param carditis_type = myo
needs:
- carditis_over12_1
outputs:
highly_sensitive:
extract: output/over12/vax1/extract/input_myocarditis_severity.feather
extract_carditis_date_over12_1_peri:
run: cohortextractor:latest generate_cohort --study-definition study_definition_carditis_severity
--output-file output/over12/vax1/extract/input_pericarditis_severity.feather
--param cohort=over12 --param vaxn=1 --param carditis_type = peri
needs:
- carditis_over12_1
outputs:
highly_sensitive:
extract: output/over12/vax1/extract/input_pericarditis_severity.feather
carditis_hosp_over12_1:
run: r:latest analysis/carditis_hospitalisation.R over12 1 both
needs:
- extract_carditis_date_over12_1_myo
- extract_carditis_date_over12_1_peri
- carditis_over12_1
outputs:
moderately_sensitive:
csv: output/over12/vax1/carditis_severity/*tables.csv
## # # # # # # # # # # # # # # # # # # #
## Covid tests data
## # # # # # # # # # # # # # # # # # # #
extract_covidtests_over12_1_treated:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covidtests
--output-file output/over12/vax1/covidtests/extract/input_covidtests_treated.feather
--param cohort=over12 --param vaxn=1 --param arm=treated
needs:
- process_controlfinal_over12_1
outputs:
highly_sensitive:
extract: output/over12/vax1/covidtests/extract/input_covidtests_treated.feather
extract_covidtests_over12_1_control:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covidtests
--output-file output/over12/vax1/covidtests/extract/input_covidtests_control.feather
--param cohort=over12 --param vaxn=1 --param arm=control
needs:
- process_controlfinal_over12_1
outputs:
highly_sensitive:
extract: output/over12/vax1/covidtests/extract/input_covidtests_control.feather
process_covidtests_over12_1:
run: r:latest analysis/covidtests/process_covidtests.R over12 1
needs:
- process_controlfinal_over12_1
- extract_covidtests_over12_1_treated
- extract_covidtests_over12_1_control
outputs:
highly_sensitive:
extract: output/over12/vax1/covidtests/process/*.rds
moderately_sensitive:
skim: output/over12/vax1/covidtests/extract/*.txt
png: output/over12/vax1/covidtests/checks/*.png
summarise_covidtests_over12_1:
run: r:latest analysis/covidtests/summarise_covidtests.R over12 1 all
needs:
- process_covidtests_over12_1
outputs:
moderately_sensitive:
csv: output/over12/vax1/covidtests/summary/all/*.csv
png: output/over12/vax1/covidtests/summary/all/*.png
## # # # # # # # # # # # # # # # # # # #
## Vax2, Over 12s cohort
## # # # # # # # # # # # # # # # # # # #
extract_treated_over12_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_treated
--output-file output/over12/vax2/extract/input_treated.feather --param cohort=over12
--param vaxn=2
outputs:
highly_sensitive:
extract: output/over12/vax2/extract/input_treated.feather
process_treated_over12_2:
run: r:latest analysis/treated/process_treated.R over12 2
needs:
- extract_treated_over12_2
outputs:
highly_sensitive:
rds: output/over12/vax2/treated/*.rds
extract_controlpotential_over12_2_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax2/matchround1/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=1 --param index_date=2021-12-13
--param vaxn=2
needs: []
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround1/extract/input_controlpotential.feather
process_controlpotential_over12_2_1:
run: r:latest analysis/matching/process_controlpotential.R over12 2 1
needs:
- extract_controlpotential_over12_2_1
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround1/process/*.rds
match_potential_over12_2_1:
run: r:latest analysis/matching/match_potential.R over12 2 1
needs:
- process_treated_over12_2
- process_controlpotential_over12_2_1
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround1/potential/*.rds
csv: output/over12/vax2/matchround1/potential/*.csv.gz
extract_controlactual_over12_2_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax2/matchround1/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=1 --param vaxn=2
needs:
- match_potential_over12_2_1
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround1/extract/input_controlactual.feather
process_controlactual_over12_2_1:
run: r:latest analysis/matching/process_controlactual.R over12 2 1
needs:
- process_treated_over12_2
- match_potential_over12_2_1
- extract_controlpotential_over12_2_1
- extract_controlactual_over12_2_1
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround1/actual/*.rds
csv: output/over12/vax2/matchround1/actual/*.csv.gz
extract_controlpotential_over12_2_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax2/matchround2/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=2 --param index_date=2021-12-27
--param vaxn=2
needs:
- process_controlactual_over12_2_1
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround2/extract/input_controlpotential.feather
process_controlpotential_over12_2_2:
run: r:latest analysis/matching/process_controlpotential.R over12 2 2
needs:
- extract_controlpotential_over12_2_2
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround2/process/*.rds
match_potential_over12_2_2:
run: r:latest analysis/matching/match_potential.R over12 2 2
needs:
- process_treated_over12_2
- process_controlpotential_over12_2_2
- process_controlactual_over12_2_1
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround2/potential/*.rds
csv: output/over12/vax2/matchround2/potential/*.csv.gz
extract_controlactual_over12_2_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax2/matchround2/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=2 --param vaxn=2
needs:
- match_potential_over12_2_2
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround2/extract/input_controlactual.feather
process_controlactual_over12_2_2:
run: r:latest analysis/matching/process_controlactual.R over12 2 2
needs:
- process_treated_over12_2
- match_potential_over12_2_2
- extract_controlpotential_over12_2_2
- extract_controlactual_over12_2_2
- process_controlactual_over12_2_1
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround2/actual/*.rds
csv: output/over12/vax2/matchround2/actual/*.csv.gz
extract_controlpotential_over12_2_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax2/matchround3/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=3 --param index_date=2022-01-10
--param vaxn=2
needs:
- process_controlactual_over12_2_2
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround3/extract/input_controlpotential.feather
process_controlpotential_over12_2_3:
run: r:latest analysis/matching/process_controlpotential.R over12 2 3
needs:
- extract_controlpotential_over12_2_3
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround3/process/*.rds
match_potential_over12_2_3:
run: r:latest analysis/matching/match_potential.R over12 2 3
needs:
- process_treated_over12_2
- process_controlpotential_over12_2_3
- process_controlactual_over12_2_2
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround3/potential/*.rds
csv: output/over12/vax2/matchround3/potential/*.csv.gz
extract_controlactual_over12_2_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax2/matchround3/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=3 --param vaxn=2
needs:
- match_potential_over12_2_3
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround3/extract/input_controlactual.feather
process_controlactual_over12_2_3:
run: r:latest analysis/matching/process_controlactual.R over12 2 3
needs:
- process_treated_over12_2
- match_potential_over12_2_3
- extract_controlpotential_over12_2_3
- extract_controlactual_over12_2_3
- process_controlactual_over12_2_2
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround3/actual/*.rds
csv: output/over12/vax2/matchround3/actual/*.csv.gz
extract_controlpotential_over12_2_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlpotential
--output-file output/over12/vax2/matchround4/extract/input_controlpotential.feather
--param cohort=over12 --param matching_round=4 --param index_date=2022-01-24
--param vaxn=2
needs:
- process_controlactual_over12_2_3
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround4/extract/input_controlpotential.feather
process_controlpotential_over12_2_4:
run: r:latest analysis/matching/process_controlpotential.R over12 2 4
needs:
- extract_controlpotential_over12_2_4
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround4/process/*.rds
match_potential_over12_2_4:
run: r:latest analysis/matching/match_potential.R over12 2 4
needs:
- process_treated_over12_2
- process_controlpotential_over12_2_4
- process_controlactual_over12_2_3
outputs:
highly_sensitive:
rds: output/over12/vax2/matchround4/potential/*.rds
csv: output/over12/vax2/matchround4/potential/*.csv.gz
extract_controlactual_over12_2_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_controlactual
--output-file output/over12/vax2/matchround4/extract/input_controlactual.feather
--param cohort=over12 --param matching_round=4 --param vaxn=2
needs:
- match_potential_over12_2_4
outputs:
highly_sensitive:
cohort: output/over12/vax2/matchround4/extract/input_controlactual.feather
process_controlactual_over12_2_4:
run: r:latest analysis/matching/process_controlactual.R over12 2 4
needs:
- process_treated_over12_2
- match_potential_over12_2_4
- extract_controlpotential_over12_2_4
- extract_controlactual_over12_2_4
- process_controlactual_over12_2_3
outputs: