generated from opensafely/covid-vaccine-research-template
/
project.yaml
1453 lines (1230 loc) · 55.7 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 50000
actions:
design:
run: r:latest analysis/R/design.R
outputs:
moderately_sensitive:
metadata: output/metadata/metadata*
chars: output/metadata/baseline_characteristics.rds
formula: output/metadata/list_formula.rds
strata: output/metadata/list_strata.rds
reweight: output/metadata/reweight_death.rds
##############################################################################
##############################################################################
## VE in over 80s (over80s)
##############################################################################
##############################################################################
extract_over80s:
run: cohortextractor:latest generate_cohort --study-definition study_definition_over80s --output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_over80s.csv.gz
data_process_over80s:
run: r:latest analysis/R/data_process.R over80s
needs: [extract_over80s]
outputs:
highly_sensitive:
data: output/over80s/data/data_processed.rds
data_process_long_over80s:
run: r:latest analysis/R/data_process_long.R over80s
needs: [data_process_over80s]
outputs:
highly_sensitive:
data1: output/over80s/data/data_long_vax_dates.rds
data2: output/over80s/data/data_long_admission_dates.rds
data3: output/over80s/data/data_long_admission_infectious_dates.rds
data4: output/over80s/data/data_long_admission_noninfectious_dates.rds
data5: output/over80s/data/data_long_pr_probable_covid_dates.rds
data6: output/over80s/data/data_long_pr_suspected_covid_dates.rds
data7: output/over80s/data/data_long_postest_dates.rds
check_ethnicity_over80s:
run: r:latest analysis/R/check_ethnicity.R over80s
needs: [data_process_over80s]
outputs:
moderately_sensitive:
tab: output/over80s/data/ethnicity_table*.txt
data_properties_over80s:
run: r:latest analysis/R/data_properties.R output/over80s/data/data_processed.rds output/over80s/data_properties
needs: [data_process_over80s]
outputs:
moderately_sensitive:
datasummary: output/over80s/data_properties/data_processed*.txt
data_selection_over80s:
run: r:latest analysis/R/data_selection.R over80s
needs: [data_process_over80s]
outputs:
highly_sensitive:
data: output/over80s/data/data_cohort.rds
moderately_sensitive:
flow: output/over80s/data/flowchart.csv
descr_table1_over80s:
run: r:latest analysis/R/descr_table1.R over80s
needs: [design, data_selection_over80s]
outputs:
highly_sensitive:
rds: output/over80s/descriptive/tables/*.rds
moderately_sensitive:
html: output/over80s/descriptive/tables/table1.html
descr_irr_over80s:
run: r:latest analysis/R/descr_tableirr.R over80s
needs: [design, data_selection_over80s]
outputs:
moderately_sensitive:
tables: output/over80s/descriptive/tables/table_irr.html
csv: output/over80s/descriptive/tables/table_irr.csv
data_stset_over80s:
run: r:latest analysis/R/data_stset.R over80s 0.1
needs: [design, data_selection_over80s, data_process_long_over80s]
outputs:
highly_sensitive:
data1: output/over80s/data/data_fixed.rds
data2: output/over80s/data/data_tte.rds
data3: output/over80s/data/data_pt.rds
data_samples_over80s:
run: r:latest analysis/R/data_samples.R over80s 0.1
needs: [design, data_stset_over80s]
outputs:
highly_sensitive:
data: output/over80s/data/data_samples.rds
descr_preflight_over80s:
run: r:latest analysis/R/preflight.R over80s all 0.15
needs: [design, data_stset_over80s]
outputs:
moderately_sensitive:
html: output/over80s/descriptive/model-checks/*.html
csv: output/over80s/descriptive/model-checks/*.csv
descr_events_over80s:
run: r:latest analysis/R/descr_events.R over80s
needs: [design, data_stset_over80s]
outputs:
highly_sensitive:
rds: output/over80s/descriptive/plots/*.rds
moderately_sensitive:
plots: output/over80s/descriptive/plots/*.svg
tables: output/over80s/descriptive/tables/*.csv
# data_properties_over80s_fixed:
# run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_fixed.rds output/over80s/data_properties
# needs: [data_stset_over80s]
# outputs:
# moderately_sensitive:
# datasummary: output/over80s/data_properties/data_wide_fixed*.txt
#
# data_properties_over80s_tte:
# run: r:latest analysis/R/data_properties.R output/over80s/data/data_wide_tte.rds output/over80s/data_properties
# needs: [data_stset_over80s]
# outputs:
# moderately_sensitive:
# datasummary: output/over80s/data_properties/data_wide_tte*.txt
#######################################
## OVERALL MODELS: positive test, vax1 only (ignores second dose)
#######################################
## any vaccine
models_over80s_postest_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/postest/any/all/*/model*.rds
data: output/over80s/postest/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/postest/any/all/*/weights*
report_ipw_over80s_postest_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s postest any all
needs: [design, models_over80s_postest_any_all]
outputs:
highly_sensitive:
broom: output/over80s/postest/any/all/*/broom*.rds
gt: output/over80s/postest/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/postest/any/all/*/plot*.svg
tables: output/over80s/postest/any/all/*/tab*.html
data: output/over80s/postest/any/all/*/broom*.csv
report_over80s_postest_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest any all
needs: [design, models_over80s_postest_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/any/all/*.svg
tables: output/over80s/postest/any/all/*.csv
## pfizer vaccine
models_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/postest/pfizer/all/*/model*.rds
data: output/over80s/postest/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/postest/pfizer/all/*/weights*
report_ipw_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s postest pfizer all
needs: [design, models_over80s_postest_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/postest/pfizer/all/*/broom*.rds
gt: output/over80s/postest/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/postest/pfizer/all/*/plot*.svg
tables: output/over80s/postest/pfizer/all/*/tab*.html
data: output/over80s/postest/pfizer/all/*/broom*.csv
report_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest pfizer all
needs: [design, models_over80s_postest_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/pfizer/all/*.svg
tables: output/over80s/postest/pfizer/all/*.csv
## az vaccine
models_over80s_postest_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/postest/az/all/*/model*.rds
data: output/over80s/postest/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/postest/az/all/*/weights*
report_ipw_over80s_postest_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s postest az all
needs: [design, models_over80s_postest_az_all]
outputs:
highly_sensitive:
broom: output/over80s/postest/az/all/*/broom*.rds
gt: output/over80s/postest/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/postest/az/all/*/plot*.svg
tables: output/over80s/postest/az/all/*/tab*.html
data: output/over80s/postest/az/all/*/broom*.csv
report_over80s_postest_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest az all
needs: [design, models_over80s_postest_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/az/all/*.svg
tables: output/over80s/postest/az/all/*.csv
#######################################
## OVERALL MODELS: covid hospital admission, vax1 only (ignores second dose)
#######################################
## any vaccine
models_over80s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/covidadmitted/any/all/*/model*.rds
data: output/over80s/covidadmitted/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/covidadmitted/any/all/*/weights*
report_ipw_over80s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted any all
needs: [design, models_over80s_covidadmitted_any_all]
outputs:
highly_sensitive:
broom: output/over80s/covidadmitted/any/all/*/broom*.rds
gt: output/over80s/covidadmitted/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/covidadmitted/any/all/*/plot*.svg
tables: output/over80s/covidadmitted/any/all/*/tab*.html
data: output/over80s/covidadmitted/any/all/*/broom*.csv
report_over80s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted any all
needs: [design, models_over80s_covidadmitted_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/covidadmitted/any/all/*.svg
tables: output/over80s/covidadmitted/any/all/*.csv
## pfizer vaccine
models_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/covidadmitted/pfizer/all/*/model*.rds
data: output/over80s/covidadmitted/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/covidadmitted/pfizer/all/*/weights*
report_ipw_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted pfizer all
needs: [design, models_over80s_covidadmitted_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/covidadmitted/pfizer/all/*/broom*.rds
gt: output/over80s/covidadmitted/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/covidadmitted/pfizer/all/*/plot*.svg
tables: output/over80s/covidadmitted/pfizer/all/*/tab*.html
data: output/over80s/covidadmitted/pfizer/all/*/broom*.csv
report_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted pfizer all
needs: [design, models_over80s_covidadmitted_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/covidadmitted/pfizer/all/*.svg
tables: output/over80s/covidadmitted/pfizer/all/*.csv
## az vaccine
models_over80s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/covidadmitted/az/all/*/model*.rds
data: output/over80s/covidadmitted/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/covidadmitted/az/all/*/weights*
report_ipw_over80s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s covidadmitted az all
needs: [design, models_over80s_covidadmitted_az_all]
outputs:
highly_sensitive:
broom: output/over80s/covidadmitted/az/all/*/broom*.rds
gt: output/over80s/covidadmitted/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/covidadmitted/az/all/*/plot*.svg
tables: output/over80s/covidadmitted/az/all/*/tab*.html
data: output/over80s/covidadmitted/az/all/*/broom*.csv
report_over80s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted az all
needs: [design, models_over80s_covidadmitted_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/covidadmitted/az/all/*.svg
tables: output/over80s/covidadmitted/az/all/*.csv
#######################################
## OVERALL MODELS: non-covid death, vax1 only (ignores second dose)
#######################################
## any vaccine
models_over80s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/noncoviddeath/any/all/*/model*.rds
data: output/over80s/noncoviddeath/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/noncoviddeath/any/all/*/weights*
report_ipw_over80s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath any all
needs: [design, models_over80s_noncoviddeath_any_all]
outputs:
highly_sensitive:
broom: output/over80s/noncoviddeath/any/all/*/broom*.rds
gt: output/over80s/noncoviddeath/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/noncoviddeath/any/all/*/plot*.svg
tables: output/over80s/noncoviddeath/any/all/*/tab*.html
data: output/over80s/noncoviddeath/any/all/*/broom*.csv
report_over80s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath any all
needs: [design, models_over80s_noncoviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/noncoviddeath/any/all/*.svg
tables: output/over80s/noncoviddeath/any/all/*.csv
## pfizer vaccine
models_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/noncoviddeath/pfizer/all/*/model*.rds
data: output/over80s/noncoviddeath/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/noncoviddeath/pfizer/all/*/weights*
report_ipw_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath pfizer all
needs: [design, models_over80s_noncoviddeath_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/noncoviddeath/pfizer/all/*/broom*.rds
gt: output/over80s/noncoviddeath/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/noncoviddeath/pfizer/all/*/plot*.svg
tables: output/over80s/noncoviddeath/pfizer/all/*/tab*.html
data: output/over80s/noncoviddeath/pfizer/all/*/broom*.csv
report_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath pfizer all
needs: [design, models_over80s_noncoviddeath_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/noncoviddeath/pfizer/all/*.svg
tables: output/over80s/noncoviddeath/pfizer/all/*.csv
## az vaccine
models_over80s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/noncoviddeath/az/all/*/model*.rds
data: output/over80s/noncoviddeath/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/noncoviddeath/az/all/*/weights*
report_ipw_over80s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s noncoviddeath az all
needs: [design, models_over80s_noncoviddeath_az_all]
outputs:
highly_sensitive:
broom: output/over80s/noncoviddeath/az/all/*/broom*.rds
gt: output/over80s/noncoviddeath/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/noncoviddeath/az/all/*/plot*.svg
tables: output/over80s/noncoviddeath/az/all/*/tab*.html
data: output/over80s/noncoviddeath/az/all/*/broom*.csv
report_over80s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath az all
needs: [design, models_over80s_noncoviddeath_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/noncoviddeath/az/all/*.svg
tables: output/over80s/noncoviddeath/az/all/*.csv
#######################################
## OVERALL MODELS: covid death, vax1 only (ignores second dose)
#######################################
## any vaccine
models_over80s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/coviddeath/any/all/*/model*.rds
data: output/over80s/coviddeath/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/coviddeath/any/all/*/weights*
report_ipw_over80s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath any all
needs: [design, models_over80s_coviddeath_any_all]
outputs:
highly_sensitive:
broom: output/over80s/coviddeath/any/all/*/broom*.rds
gt: output/over80s/coviddeath/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/coviddeath/any/all/*/plot*.svg
tables: output/over80s/coviddeath/any/all/*/tab*.html
data: output/over80s/coviddeath/any/all/*/broom*.csv
report_over80s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath any all
needs: [design, models_over80s_coviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/coviddeath/any/all/*.svg
tables: output/over80s/coviddeath/any/all/*.csv
## pfizer vaccine
models_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/coviddeath/pfizer/all/*/model*.rds
data: output/over80s/coviddeath/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/coviddeath/pfizer/all/*/weights*
report_ipw_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath pfizer all
needs: [design, models_over80s_coviddeath_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/coviddeath/pfizer/all/*/broom*.rds
gt: output/over80s/coviddeath/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/coviddeath/pfizer/all/*/plot*.svg
tables: output/over80s/coviddeath/pfizer/all/*/tab*.html
data: output/over80s/coviddeath/pfizer/all/*/broom*.csv
report_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath pfizer all
needs: [design, models_over80s_coviddeath_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/coviddeath/pfizer/all/*.svg
tables: output/over80s/coviddeath/pfizer/all/*.csv
## az vaccine
models_over80s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/coviddeath/az/all/*/model*.rds
data: output/over80s/coviddeath/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/coviddeath/az/all/*/weights*
report_ipw_over80s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s coviddeath az all
needs: [design, models_over80s_coviddeath_az_all]
outputs:
highly_sensitive:
broom: output/over80s/coviddeath/az/all/*/broom*.rds
gt: output/over80s/coviddeath/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/coviddeath/az/all/*/plot*.svg
tables: output/over80s/coviddeath/az/all/*/tab*.html
data: output/over80s/coviddeath/az/all/*/broom*.csv
report_over80s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath az all
needs: [design, models_over80s_coviddeath_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/coviddeath/az/all/*.svg
tables: output/over80s/coviddeath/az/all/*.csv
#######################################
## OVERALL MODELS: all-cause death, vax1 only (ignores second dose)
#######################################
## any vaccine
models_over80s_death_any_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s death any all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/death/any/all/*/model*.rds
data: output/over80s/death/any/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/death/any/all/*/weights*
report_ipw_over80s_death_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s death any all
needs: [design, models_over80s_death_any_all]
outputs:
highly_sensitive:
broom: output/over80s/death/any/all/*/broom*.rds
gt: output/over80s/death/any/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/death/any/all/*/plot*.svg
tables: output/over80s/death/any/all/*/tab*.html
data: output/over80s/death/any/all/*/broom*.csv
report_over80s_death_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death any all
needs: [design, models_over80s_death_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/any/all/*.svg
tables: output/over80s/death/any/all/*.csv
## pfizer vaccine
models_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s death pfizer all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/death/pfizer/all/*/model*.rds
data: output/over80s/death/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/death/pfizer/all/*/weights*
report_ipw_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s death pfizer all
needs: [design, models_over80s_death_pfizer_all]
outputs:
highly_sensitive:
broom: output/over80s/death/pfizer/all/*/broom*.rds
gt: output/over80s/death/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/death/pfizer/all/*/plot*.svg
tables: output/over80s/death/pfizer/all/*/tab*.html
data: output/over80s/death/pfizer/all/*/broom*.csv
report_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death pfizer all
needs: [design, models_over80s_death_pfizer_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/pfizer/all/*.svg
tables: output/over80s/death/pfizer/all/*.csv
## az vaccine
models_over80s_death_az_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s death az all
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/death/az/all/*/model*.rds
data: output/over80s/death/az/all/*/data*.rds
moderately_sensitive:
weights: output/over80s/death/az/all/*/weights*
report_ipw_over80s_death_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R over80s death az all
needs: [design, models_over80s_death_az_all]
outputs:
highly_sensitive:
broom: output/over80s/death/az/all/*/broom*.rds
gt: output/over80s/death/az/all/*/gt*.rds
moderately_sensitive:
plots: output/over80s/death/az/all/*/plot*.svg
tables: output/over80s/death/az/all/*/tab*.html
data: output/over80s/death/az/all/*/broom*.csv
report_over80s_death_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death az all
needs: [design, models_over80s_death_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/az/all/*.svg
tables: output/over80s/death/az/all/*.csv
#######################################
## IMMUNOSUPPRESSION MODELS: positive test, vax1 only (ignores second dose)
#######################################
## any vaccine
models_over80s_postest_any_immuno:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest any any_immunosuppression
needs: [design, data_stset_over80s, data_samples_over80s]
outputs:
highly_sensitive:
models: output/over80s/postest/any/any_immunosuppression/*/model*.rds
data: output/over80s/postest/any/any_immunosuppression/*/data*.rds
moderately_sensitive:
weights: output/over80s/postest/any/any_immunosuppression/*/weights*
report_ipw_over80s_postest_any_immuno:
run: r:latest analysis/R/dose_1/report_ipw.R over80s postest any any_immunosuppression
needs: [design, models_over80s_postest_any_immuno]
outputs:
highly_sensitive:
broom: output/over80s/postest/any/any_immunosuppression/*/broom*.rds
gt: output/over80s/postest/any/any_immunosuppression/*/gt*.rds
moderately_sensitive:
plots: output/over80s/postest/any/any_immunosuppression/*/plot*.svg
tables: output/over80s/postest/any/any_immunosuppression/*/tab*.html
data: output/over80s/postest/any/any_immunosuppression/*/broom*.csv
report_over80s_postest_any_immuno:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest any any_immunosuppression
needs: [design, models_over80s_postest_any_immuno]
outputs:
moderately_sensitive:
plots: output/over80s/postest/any/any_immunosuppression/*.svg
tables: output/over80s/postest/any/any_immunosuppression/*.csv
#######################################
## COMBINE OVERALL MODELS:
#######################################
# report_over80s_any_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s any all
# needs: [design, report_over80s_postest_any_all, report_over80s_covidadmitted_any_all, report_over80s_coviddeath_any_all, report_over80s_noncoviddeath_any_all, report_over80s_death_any_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/*any_all.svg
# tables: output/over80s/*any_all.csv
# html: output/over80s/*any_all.html
#
# report_over80s_pfizer_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s pfizer all
# needs: [design, report_over80s_postest_pfizer_all, report_over80s_covidadmitted_pfizer_all, report_over80s_coviddeath_pfizer_all, report_over80s_noncoviddeath_pfizer_all, report_over80s_death_pfizer_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/*pfizer_all.svg
# tables: output/over80s/*pfizer_all.csv
# html: output/over80s/*pfizer_all.html
#
# report_over80s_az_all:
# run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s az all
# needs: [design, report_over80s_postest_az_all, report_over80s_covidadmitted_az_all, report_over80s_coviddeath_az_all, report_over80s_noncoviddeath_az_all, report_over80s_death_az_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/*az_all.svg
# tables: output/over80s/*az_all.csv
# html: output/over80s/*az_all.html
report_ipw_over80s_all:
run: r:latest analysis/R/dose_1/report_vaxmodel.R over80s death all
needs: [design, report_ipw_over80s_death_any_all, report_ipw_over80s_death_pfizer_all, report_ipw_over80s_death_az_all]
outputs:
moderately_sensitive:
svg: output/over80s/plot_vax1.svg
#html: output/over80s/tab_vax1.html
csv: output/over80s/tab_vax1.csv
csv1: output/over80s/tab_vax1_wide.csv
report_over80s_all:
run: r:latest analysis/R/dose_1/report_alloutcomes_combined.R over80s all
needs: [design, report_over80s_postest_any_all, report_over80s_covidadmitted_any_all, report_over80s_coviddeath_any_all, report_over80s_noncoviddeath_any_all, report_over80s_death_any_all,
report_over80s_postest_pfizer_all, report_over80s_covidadmitted_pfizer_all, report_over80s_coviddeath_pfizer_all, report_over80s_noncoviddeath_pfizer_all, report_over80s_death_pfizer_all,
report_over80s_postest_az_all, report_over80s_covidadmitted_az_all, report_over80s_coviddeath_az_all, report_over80s_noncoviddeath_az_all, report_over80s_death_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/*_all.svg
plots1: output/over80s/*_all.png
tables: output/over80s/*_all.csv
##############################################################################
##############################################################################
## VE in 70-79s
##############################################################################
##############################################################################
extract_in70s:
run: cohortextractor:latest generate_cohort --study-definition study_definition_in70s --output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_in70s.csv.gz
data_process_in70s:
run: r:latest analysis/R/data_process.R in70s
needs: [extract_in70s]
outputs:
highly_sensitive:
data: output/in70s/data/data_processed.rds
data_process_long_in70s:
run: r:latest analysis/R/data_process_long.R in70s
needs: [data_process_in70s]
outputs:
highly_sensitive:
data1: output/in70s/data/data_long_vax_dates.rds
data2: output/in70s/data/data_long_admission_dates.rds
data3: output/in70s/data/data_long_admission_infectious_dates.rds
data4: output/in70s/data/data_long_admission_noninfectious_dates.rds
data5: output/in70s/data/data_long_pr_probable_covid_dates.rds
data6: output/in70s/data/data_long_pr_suspected_covid_dates.rds
data7: output/in70s/data/data_long_postest_dates.rds
check_ethnicity_in70s:
run: r:latest analysis/R/check_ethnicity.R in70s
needs: [data_process_in70s]
outputs:
moderately_sensitive:
tab: output/in70s/data/ethnicity_table*.txt
data_properties_in70s:
run: r:latest analysis/R/data_properties.R output/in70s/data/data_processed.rds output/in70s/data_properties
needs: [data_process_in70s]
outputs:
moderately_sensitive:
datasummary: output/in70s/data_properties/data_processed*.txt
data_selection_in70s:
run: r:latest analysis/R/data_selection.R in70s
needs: [data_process_in70s]
outputs:
highly_sensitive:
data: output/in70s/data/data_cohort.rds
moderately_sensitive:
flow: output/in70s/data/flowchart.csv
descr_table1_in70s:
run: r:latest analysis/R/descr_table1.R in70s
needs: [design, data_selection_in70s]
outputs:
highly_sensitive:
rds: output/in70s/descriptive/tables/*.rds
moderately_sensitive:
html: output/in70s/descriptive/tables/table1.html
descr_irr_in70s:
run: r:latest analysis/R/descr_tableirr.R in70s
needs: [design, data_selection_in70s]
outputs:
moderately_sensitive:
tables: output/in70s/descriptive/tables/table_irr.html
csv: output/in70s/descriptive/tables/table_irr.csv
data_stset_in70s:
run: r:latest analysis/R/data_stset.R in70s 0.05
needs: [design, data_selection_in70s, data_process_long_in70s]
outputs:
highly_sensitive:
data1: output/in70s/data/data_fixed.rds
data2: output/in70s/data/data_tte.rds
data3: output/in70s/data/data_pt.rds
data_samples_in70s:
run: r:latest analysis/R/data_samples.R in70s 0.05
needs: [design, data_stset_in70s]
outputs:
highly_sensitive:
data: output/in70s/data/data_samples.rds
descr_preflight_in70s:
run: r:latest analysis/R/preflight.R in70s all 0.05
needs: [design, data_stset_in70s]
outputs:
moderately_sensitive:
html: output/in70s/descriptive/model-checks/*.html
csv: output/in70s/descriptive/model-checks/*.csv
descr_events_in70s:
run: r:latest analysis/R/descr_events.R in70s
needs: [design, data_stset_in70s]
outputs:
highly_sensitive:
rds: output/in70s/descriptive/plots/*.rds
moderately_sensitive:
plots: output/in70s/descriptive/plots/*.svg
tables: output/in70s/descriptive/tables/*.csv
# data_properties_in70s_fixed:
# run: r:latest analysis/R/data_properties.R output/in70s/data/data_wide_fixed.rds output/in70s/data_properties
# needs: [data_stset_in70s]
# outputs:
# moderately_sensitive:
# datasummary: output/in70s/data_properties/data_wide_fixed*.txt
#
# data_properties_in70s_tte:
# run: r:latest analysis/R/data_properties.R output/in70s/data/data_wide_tte.rds output/in70s/data_properties
# needs: [data_stset_in70s]
# outputs:
# moderately_sensitive:
# datasummary: output/in70s/data_properties/data_wide_tte*.txt
#######################################
## OVERALL MODELS: positive test, vax1 only (ignores second dose)
#######################################
## any vaccine
models_in70s_postest_any_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s postest any all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/postest/any/all/*/model*.rds
data: output/in70s/postest/any/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/postest/any/all/*/weights*
report_ipw_in70s_postest_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s postest any all
needs: [design, models_in70s_postest_any_all]
outputs:
highly_sensitive:
broom: output/in70s/postest/any/all/*/broom*.rds
gt: output/in70s/postest/any/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/postest/any/all/*/plot*.svg
tables: output/in70s/postest/any/all/*/tab*.html
data: output/in70s/postest/any/all/*/broom*.csv
report_in70s_postest_any_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s postest any all
needs: [design, models_in70s_postest_any_all]
outputs:
moderately_sensitive:
plots: output/in70s/postest/any/all/*.svg
tables: output/in70s/postest/any/all/*.csv
## pfizer vaccine
models_in70s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s postest pfizer all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/postest/pfizer/all/*/model*.rds
data: output/in70s/postest/pfizer/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/postest/pfizer/all/*/weights*
report_ipw_in70s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s postest pfizer all
needs: [design, models_in70s_postest_pfizer_all]
outputs:
highly_sensitive:
broom: output/in70s/postest/pfizer/all/*/broom*.rds
gt: output/in70s/postest/pfizer/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/postest/pfizer/all/*/plot*.svg
tables: output/in70s/postest/pfizer/all/*/tab*.html
data: output/in70s/postest/pfizer/all/*/broom*.csv
report_in70s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s postest pfizer all
needs: [design, models_in70s_postest_pfizer_all]
outputs:
moderately_sensitive:
plots: output/in70s/postest/pfizer/all/*.svg
tables: output/in70s/postest/pfizer/all/*.csv
## az vaccine
models_in70s_postest_az_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s postest az all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/postest/az/all/*/model*.rds
data: output/in70s/postest/az/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/postest/az/all/*/weights*
report_ipw_in70s_postest_az_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s postest az all
needs: [design, models_in70s_postest_az_all]
outputs:
highly_sensitive:
broom: output/in70s/postest/az/all/*/broom*.rds
gt: output/in70s/postest/az/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/postest/az/all/*/plot*.svg
tables: output/in70s/postest/az/all/*/tab*.html
data: output/in70s/postest/az/all/*/broom*.csv
report_in70s_postest_az_all:
run: r:latest analysis/R/dose_1/report_msm.R in70s postest az all
needs: [design, models_in70s_postest_az_all]
outputs:
moderately_sensitive:
plots: output/in70s/postest/az/all/*.svg
tables: output/in70s/postest/az/all/*.csv
#######################################
## OVERALL MODELS: covid hospital admission, vax1 only (ignores second dose)
#######################################
## any vaccine
models_in70s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/model_msm.R in70s covidadmitted any all
needs: [design, data_stset_in70s, data_samples_in70s]
outputs:
highly_sensitive:
models: output/in70s/covidadmitted/any/all/*/model*.rds
data: output/in70s/covidadmitted/any/all/*/data*.rds
moderately_sensitive:
weights: output/in70s/covidadmitted/any/all/*/weights*
report_ipw_in70s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_ipw.R in70s covidadmitted any all
needs: [design, models_in70s_covidadmitted_any_all]
outputs:
highly_sensitive:
broom: output/in70s/covidadmitted/any/all/*/broom*.rds
gt: output/in70s/covidadmitted/any/all/*/gt*.rds
moderately_sensitive:
plots: output/in70s/covidadmitted/any/all/*/plot*.svg