generated from opensafely/covid-vaccine-research-template
/
project.yaml
1810 lines (1528 loc) · 69.1 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 500000
actions:
extract_all:
run: cohortextractor:latest generate_cohort --study-definition study_definition_all --output-format csv.gz
outputs:
highly_sensitive:
cohort: output/input_all.csv.gz
generate_over80s_flow_chart_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_over80s_flow_chart
outputs:
highly_sensitive:
cohort: output/input_over80s_flow_chart.csv
flow_chart_over80s:
run: r:latest -e 'rmarkdown::render("analysis/R/study_definition_over80s_flow_chart.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
needs: [generate_over80s_flow_chart_data]
outputs:
moderately_sensitive:
html: output/study_definition_over80s_flow_chart.html
data_process_all:
run: r:latest analysis/R/data_process_all.R
needs: [extract_all]
outputs:
highly_sensitive:
data1: output/data/data_all.rds
data2: output/data/data_long_vax_dates.rds
data3: output/data/data_long_admission_dates.rds
data4: output/data/data_long_admission_infectious_dates.rds
data5: output/data/data_long_admission_noninfectious_dates.rds
data6: output/data/data_long_pr_probable_covid_dates.rds
data7: output/data/data_long_pr_suspected_covid_dates.rds
data8: output/data/data_long_postest_dates.rds
check_ethnicity:
run: r:latest analysis/R/check_ethnicity.R
needs: [data_process_all]
outputs:
moderately_sensitive:
tab: output/data/ethnicity_table*.txt
data_properties_all:
run: r:latest analysis/R/data_properties.R output/data/data_all.rds output/data_properties
needs: [data_process_all]
outputs:
moderately_sensitive:
datasummary: output/data_properties/data_all*.txt
data_define_cohorts:
run: r:latest analysis/R/data_define_cohorts.R
needs: [data_process_all]
outputs:
highly_sensitive:
data: output/data/data_cohorts.rds
moderately_sensitive:
metadata: output/data/metadata*
formula: output/data/list_formula.rds
strata: output/data/list_strata.rds
flow: output/data/flowchart*.csv
descr_table1_over70s:
run: r:latest analysis/R/table1_light.R over70s
needs: [data_define_cohorts, data_process_all]
outputs:
moderately_sensitive:
table1: output/over70s/descr/tables/table*
descr_events_over70s:
run: r:latest analysis/R/plot_status_over_time_all.R over70s
needs: [data_define_cohorts, data_process_all]
outputs:
moderately_sensitive:
plots: output/over70s/descr/plots/*.svg
tables: output/over70s/descr/tables/*.csv
##############################################################################
##############################################################################
## VE in over 80s (over80s)
##############################################################################
##############################################################################
data_stset_over80s:
run: r:latest analysis/R/data_stset.R over80s
needs: [data_define_cohorts, data_process_all]
outputs:
highly_sensitive:
data: output/over80s/data/data_*.rds
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
descr_table1_over80s:
run: r:latest analysis/R/table1_light.R over80s
needs: [data_define_cohorts, data_process_all]
outputs:
moderately_sensitive:
table1: output/over80s/descr/tables/table*
descr_events_over80s:
run: r:latest analysis/R/plot_status_over_time_all.R over80s
needs: [data_define_cohorts, data_process_all]
outputs:
moderately_sensitive:
plots: output/over80s/descr/plots/*.svg
tables: output/over80s/descr/tables/*.csv
#######################################
## COX VACCINE MODELS
#######################################
# vaxmodels_cox_over80s_all:
# run: r:latest analysis/R/vax/vaxmodel_cox.R over80s all
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# data: output/over80s/vaccination/all/*/data_cox_sub.rds
# models: output/over80s/vaccination/all/*/vaxmodelcox*.rds
#
# vaxreport_over80s_all:
# run: r:latest analysis/R/vax/vaxreport_cox.R over80s all
# needs: [data_define_cohorts, vaxmodels_cox_over80s_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/vaccination/all/*/plot*.svg
# tables: output/over80s/vaccination/all/*/tab*.html
# data: output/over80s/vaccination/all/*/tab*.csv
#######################################
## 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_postest_any_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_postest_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest any all
needs: [data_define_cohorts, models_over80s_postest_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/any/all/*.svg
tables: output/over80s/postest/any/all/*.csv
#
# models_cox_over80s_postest_any_all_all:
# run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all all
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/postest/any/all/*/all/modelcox*.rds
#
# report_cox_over80s_postest_any_all_all:
# run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all all
# needs: [data_define_cohorts, models_cox_over80s_postest_any_all_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/postest/any/all/*cox_all.svg
# tables: output/over80s/postest/any/all/*cox_all.csv
#
# models_cox_over80s_postest_any_all_region:
# run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all region
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/postest/any/all/*/region/modelcox*.rds
#
# report_cox_over80s_postest_any_all_region:
# run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all region
# needs: [data_define_cohorts, models_cox_over80s_postest_any_all_region]
# outputs:
# moderately_sensitive:
# plots: output/over80s/postest/any/all/*cox_region.svg
# tables: output/over80s/postest/any/all/*cox_region.csv
#
# models_cox_over80s_postest_any_all_stp:
# run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all stp
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/postest/any/all/*/stp/modelcox*.rds
#
# report_cox_over80s_postest_any_all_stp:
# run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all stp
# needs: [data_define_cohorts, models_cox_over80s_postest_any_all_stp]
# outputs:
# moderately_sensitive:
# plots: output/over80s/postest/any/all/*cox_stp.svg
# tables: output/over80s/postest/any/all/*cox_stp.csv
#
# models_cox_over80s_postest_any_all_msoa:
# run: r:latest analysis/R/dose_1/model_cox.R over80s postest any all msoa
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/postest/any/all/*/msoa/modelcox*.rds
#
# report_cox_over80s_postest_any_all_msoa:
# run: r:latest analysis/R/dose_1/report_cox.R over80s postest any all msoa
# needs: [data_define_cohorts, models_cox_over80s_postest_any_all_msoa]
# outputs:
# moderately_sensitive:
# plots: output/over80s/postest/any/all/*cox_msoa.svg
# tables: output/over80s/postest/any/all/*cox_msoa.csv
#
## pfizer vaccine
models_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s postest pfizer all
needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_postest_pfizer_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_postest_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest pfizer all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_postest_az_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_postest_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s postest az all
needs: [data_define_cohorts, models_over80s_postest_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/postest/az/all/*.svg
tables: output/over80s/postest/az/all/*.csv
#
# #######################################
# ## OVERALL MODELS: emergency attendance, vax1 only (ignores second dose)
# #######################################
#
# ## any vaccine
#
# models_over80s_emergency_any_all:
# run: r:latest analysis/R/dose_1/model_msm.R over80s emergency any all
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/emergency/any/all/*/model*.rds
# data: output/over80s/emergency/any/all/*/data*.rds
# moderately_sensitive:
# weights: output/over80s/emergency/any/all/*/weights*
#
# report_ipw_over80s_emergency_any_all:
# run: r:latest analysis/R/dose_1/report_ipw.R over80s emergency any all
# needs: [data_define_cohorts, models_over80s_emergency_any_all]
# outputs:
# highly_sensitive:
# gt: output/over80s/emergency/any/all/*/gt*.rds
# moderately_sensitive:
# plots: output/over80s/emergency/any/all/*/plot*.svg
# tables: output/over80s/emergency/any/all/*/tab*.html
# data: output/over80s/emergency/any/all/*/tab*.csv
#
# report_over80s_emergency_any_all:
# run: r:latest analysis/R/dose_1/report_msm.R over80s emergency any all
# needs: [data_define_cohorts, models_over80s_emergency_any_all]
# outputs:
# moderately_sensitive:
# plots: output/over80s/emergency/any/all/*.svg
# tables: output/over80s/emergency/any/all/*.csv
# models_cox_over80s_emergency_any_all_region:
# run: r:latest analysis/R/dose_1/model_cox.R over80s emergency any all region
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/emergency/any/all/*/region/modelcox*.rds
#
# report_cox_over80s_emergency_any_all_region:
# run: r:latest analysis/R/dose_1/report_cox.R over80s emergency any all region
# needs: [data_define_cohorts, models_cox_over80s_emergency_any_all_region]
# outputs:
# moderately_sensitive:
# plots: output/over80s/emergency/any/all/*cox_region.svg
# tables: output/over80s/emergency/any/all/*cox_region.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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_covidadmitted_any_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_covidadmitted_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted any all
needs: [data_define_cohorts, models_over80s_covidadmitted_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/covidadmitted/any/all/*.svg
tables: output/over80s/covidadmitted/any/all/*.csv
# models_cox_over80s_covidadmitted_any_all_region:
# run: r:latest analysis/R/dose_1/model_cox.R over80s covidadmitted any all region
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/covidadmitted/any/all/*/region/modelcox*.rds
#
# report_cox_over80s_covidadmitted_any_all_region:
# run: r:latest analysis/R/dose_1/report_cox.R over80s covidadmitted any all region
# needs: [data_define_cohorts, models_cox_over80s_covidadmitted_any_all_region]
# outputs:
# moderately_sensitive:
# plots: output/over80s/covidadmitted/any/all/*cox_region.svg
# tables: output/over80s/covidadmitted/any/all/*cox_region.csv
## pfizer vaccine
models_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s covidadmitted pfizer all
needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_covidadmitted_pfizer_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_covidadmitted_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted pfizer all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_covidadmitted_az_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_covidadmitted_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s covidadmitted az all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_noncoviddeath_any_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_noncoviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath any all
needs: [data_define_cohorts, models_over80s_noncoviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/noncoviddeath/any/all/*.svg
tables: output/over80s/noncoviddeath/any/all/*.csv
# models_cox_over80s_noncoviddeath_any_all_region:
# run: r:latest analysis/R/dose_1/model_cox.R over80s noncoviddeath any all region
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/noncoviddeath/any/all/*/region/modelcox*.rds
#
# report_cox_over80s_noncoviddeath_any_all_region:
# run: r:latest analysis/R/dose_1/report_cox.R over80s noncoviddeath any all region
# needs: [data_define_cohorts, models_cox_over80s_noncoviddeath_any_all_region]
# outputs:
# moderately_sensitive:
# plots: output/over80s/noncoviddeath/any/all/*cox_region.svg
# tables: output/over80s/noncoviddeath/any/all/*cox_region.csv
## pfizer vaccine
models_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s noncoviddeath pfizer all
needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_noncoviddeath_pfizer_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_noncoviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath pfizer all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_noncoviddeath_az_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_noncoviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s noncoviddeath az all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_over80s]
outputs:
highly_sensitive:
models: output/over80s/coviddeath/any/all/*/model*.rds
data: output/over80s/coviddeath/any/all/*/data*.rds
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: [data_define_cohorts, models_over80s_coviddeath_any_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_coviddeath_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath any all
needs: [data_define_cohorts, models_over80s_coviddeath_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/coviddeath/any/all/*.svg
tables: output/over80s/coviddeath/any/all/*.csv
# models_cox_over80s_coviddeath_any_all_region:
# run: r:latest analysis/R/dose_1/model_cox.R over80s coviddeath any all region
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/coviddeath/any/all/*/region/modelcox*.rds
#
# report_cox_over80s_coviddeath_any_all_region:
# run: r:latest analysis/R/dose_1/report_cox.R over80s coviddeath any all region
# needs: [data_define_cohorts, models_cox_over80s_coviddeath_any_all_region]
# outputs:
# moderately_sensitive:
# plots: output/over80s/coviddeath/any/all/*cox_region.svg
# tables: output/over80s/coviddeath/any/all/*cox_region.csv
## pfizer vaccine
models_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s coviddeath pfizer all
needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_coviddeath_pfizer_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_coviddeath_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath pfizer all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_coviddeath_az_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_coviddeath_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s coviddeath az all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_death_any_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_death_any_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death any all
needs: [data_define_cohorts, models_over80s_death_any_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/any/all/*.svg
tables: output/over80s/death/any/all/*.csv
# models_cox_over80s_death_any_all_region:
# run: r:latest analysis/R/dose_1/model_cox.R over80s death any all region
# needs: [data_define_cohorts, data_stset_over80s]
# outputs:
# highly_sensitive:
# models: output/over80s/death/any/all/*/region/modelcox*.rds
#
# report_cox_over80s_death_any_all_region:
# run: r:latest analysis/R/dose_1/report_cox.R over80s death any all region
# needs: [data_define_cohorts, models_cox_over80s_death_any_all_region]
# outputs:
# moderately_sensitive:
# plots: output/over80s/death/any/all/*cox_region.svg
# tables: output/over80s/death/any/all/*cox_region.csv
## pfizer vaccine
models_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/model_msm.R over80s death pfizer all
needs: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_death_pfizer_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_death_pfizer_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death pfizer all
needs: [data_define_cohorts, 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: [data_define_cohorts, data_stset_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: [data_define_cohorts, models_over80s_death_az_all]
outputs:
highly_sensitive:
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/*/tab*.csv
report_over80s_death_az_all:
run: r:latest analysis/R/dose_1/report_msm.R over80s death az all
needs: [data_define_cohorts, models_over80s_death_az_all]
outputs:
moderately_sensitive:
plots: output/over80s/death/az/all/*.svg
tables: output/over80s/death/az/all/*.csv
#
# #######################################
# #######################################
# ## SUBGROUPS
# #######################################
# #######################################
#
# #######################################
# ## sex positive test, vax1 only (ignores second dose)
# #######################################
#
# ## any vaccine
# #
# # models_over80s_postest_any_sex:
# # run: r:latest analysis/R/dose_1/model_msm.R over80s postest any sex
# # needs: [data_define_cohorts, data_stset_over80s]
# # outputs:
# # highly_sensitive:
# # models: output/over80s/postest/any/sex/*/model*.rds
# # data: output/over80s/postest/any/sex/*/data_weights.rds
# # weights: output/over80s/postest/any/sex/*/weights*
# #
# # report_over80s_postest_any_sex:
# # run: r:latest analysis/R/dose_1/report_msm.R over80s postest any sex
# # needs: [data_define_cohorts, models_over80s_postest_any_sex]
# # outputs:
# # moderately_sensitive:
# # plots: output/over80s/postest/any/sex/*.svg
# # tables: output/over80s/postest/any/sex/*.csv
# #
# #
# # ## pfizer vaccine
# # models_over80s_postest_pfizer_sex:
# # run: r:latest analysis/R/dose_1/model_msm.R over80s postest pfizer sex
# # needs: [data_define_cohorts, data_stset_over80s]
# # outputs:
# # highly_sensitive:
# # models: output/over80s/postest/pfizer/sex/*/model*.rds
# # data: output/over80s/postest/pfizer/sex/*/data_weights.rds
# # weights: output/over80s/postest/pfizer/sex/*/weights*
# #
# # report_over80s_postest_pfizer_sex:
# # run: r:latest analysis/R/dose_1/report_msm.R over80s postest pfizer sex
# # needs: [data_define_cohorts, models_over80s_postest_pfizer_sex]
# # outputs:
# # moderately_sensitive:
# # plots: output/over80s/postest/pfizer/sex/*.svg
# # tables: output/over80s/postest/pfizer/sex/*.csv
# #
# #
# # ## az vaccine
# #
# # models_over80s_postest_az_sex:
# # run: r:latest analysis/R/dose_1/model_msm.R over80s postest az sex
# # needs: [data_define_cohorts, data_stset_over80s]
# # outputs:
# # highly_sensitive:
# # models: output/over80s/postest/az/sex/*/model*.rds
# # data: output/over80s/postest/az/sex/*/data_weights.rds
# # weights: output/over80s/postest/az/sex/*/weights*
# #
# #
# # report_over80s_postest_az_sex:
# # run: r:latest analysis/R/dose_1/report_msm.R over80s postest az sex
# # needs: [data_define_cohorts, models_over80s_postest_az_sex]
# # outputs:
# # moderately_sensitive:
# # plots: output/over80s/postest/az/sex/*.svg
# # tables: output/over80s/postest/az/sex/*.csv
# #
# #
#
#######################################
## COMBINE OVERALL MODELS:
#######################################
report_over80s_any_all:
run: r:latest analysis/R/dose_1/report_alloutcomes.R over80s any all
needs: [data_define_cohorts, 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: [data_define_cohorts, 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: [data_define_cohorts, 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_any_all:
run: r:latest analysis/R/dose_1/report_allipw.R over80s any all
needs: [data_define_cohorts, report_ipw_over80s_postest_any_all, report_ipw_over80s_covidadmitted_any_all, report_ipw_over80s_coviddeath_any_all, report_ipw_over80s_noncoviddeath_any_all, report_ipw_over80s_death_any_all]
outputs:
moderately_sensitive:
svg: output/over80s/plot_vaxany1.svg
html: output/over80s/tab_vaxany1.html
report_ipw_over80s_pfizer_all:
run: r:latest analysis/R/dose_1/report_allipw.R over80s pfizer all
needs: [data_define_cohorts, report_ipw_over80s_postest_pfizer_all, report_ipw_over80s_covidadmitted_pfizer_all, report_ipw_over80s_coviddeath_pfizer_all, report_ipw_over80s_noncoviddeath_pfizer_all, report_ipw_over80s_death_pfizer_all]
outputs:
moderately_sensitive:
svg: output/over80s/plot_vaxpfizer1.svg
html: output/over80s/tab_vaxpfizer1.html
report_ipw_over80s_az_all:
run: r:latest analysis/R/dose_1/report_allipw.R over80s az all
needs: [data_define_cohorts, report_ipw_over80s_postest_az_all, report_ipw_over80s_covidadmitted_az_all, report_ipw_over80s_coviddeath_az_all, report_ipw_over80s_noncoviddeath_az_all, report_ipw_over80s_death_az_all]
outputs:
moderately_sensitive:
svg: output/over80s/plot_vaxaz1.svg
html: output/over80s/tab_vaxaz1.html
report_ipw_over80s_all:
run: r:latest analysis/R/dose_1/report_vaxmodel.R over80s all
needs: [data_define_cohorts, 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
##############################################################################
##############################################################################
## VE in over 70s (in70s)
##############################################################################
##############################################################################
data_stset_in70s:
run: r:latest analysis/R/data_stset.R in70s
needs: [data_define_cohorts, data_process_all]
outputs:
highly_sensitive:
data: output/in70s/data/data_*.rds
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]