generated from opensafely/research-template
/
project.yaml
1341 lines (1161 loc) · 50.5 KB
/
project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml
## This file is created by create_project.R
## Edit and run create_project.R to update the project.yaml
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## ####################################
## study definition
## ####################################
## generate dummy data for study_definition
dummy_data_vax:
run: r:latest analysis/dummy_data_vax.R
outputs:
moderately_sensitive:
dummy_data: analysis/dummy_data_vax.feather
## study definition
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format feather
dummy_data_file: analysis/dummy_data_vax.feather
needs:
- dummy_data_vax
outputs:
highly_sensitive:
cohort: output/input_vax.feather
## ####################################
## preprocessing
## ####################################
## process data from study_definition
data_input_process:
run: r:latest analysis/preprocess/data_input_process.R
needs:
- dummy_data_vax
- generate_study_population
outputs:
highly_sensitive:
data_wide_vax_dates: output/data/data_wide_vax_dates.rds
data_processed: output/data/data_processed.rds
moderately_sensitive:
data_properties: output/tables/data_*_tabulate.txt
## apply eligiblity criteria from boxes a and b
data_eligible_ab:
run: r:latest analysis/preprocess/data_eligible_ab.R
needs:
- data_input_process
outputs:
highly_sensitive:
data_eligible_a: output/data/data_eligible_a.rds
data_eligible_b: output/data/data_eligible_b.rds
moderately_sensitive:
eligibility_count_ab: output/tables/eligibility_count_ab.csv
group_age_ranges: output/lib/group_age_ranges.csv
## ####################################
## second_vax_period
## ####################################
## identify second vaccination time periods
## create dataset for identifying second vaccination time periods
data_2nd_vax_dates:
run: r:latest analysis/second_vax_period/data_2nd_vax_dates.R
needs:
- data_input_process
- data_eligible_ab
outputs:
highly_sensitive:
data_vax_plot: output/second_vax_period/data/data_vax_plot.rds
second_vax_period_dates_rds: output/second_vax_period/data/second_vax_period_dates.rds
moderately_sensitive:
second_vax_period_dates_txt: output/second_vax_period/tables/second_vax_period_dates.txt
## plot second vaccination time periods
plot_2nd_vax_dates:
run: r:latest analysis/second_vax_period/plot_2nd_vax_dates.R
needs:
- data_eligible_ab
- data_2nd_vax_dates
outputs:
moderately_sensitive:
plots_by_region: output/second_vax_period/images/plot_by_region_*.png
plots_by_region_data: output/second_vax_period/images/plot_by_region_*.txt
## apply eligiblity criteria from boxes c, d and e
data_eligible_cde:
run: r:latest analysis/preprocess/data_eligible_cde.R
needs:
- data_input_process
- data_eligible_ab
- data_2nd_vax_dates
outputs:
highly_sensitive:
data_eligible_e_vax: output/data/data_eligible_e_vax.rds
data_eligible_e_unvax: output/data/data_eligible_e_unvax.rds
data_eligible_e: output/data/data_eligible_e.csv
moderately_sensitive:
eligibility_count_cde: output/tables/eligibility_count_cde.csv
## ####################################
## study definition covs
## ####################################
generate_covs_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_covs
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_covs.feather
## ####################################
## process covariates data
## ####################################
## (includes anytest_date)
data_covariates_process:
run: r:latest analysis/preprocess/data_covariates_process.R
needs:
- data_input_process
- data_eligible_cde
- generate_covs_data
outputs:
highly_sensitive:
data_covariates: output/data/data_all.rds
moderately_sensitive:
data_min_max_fu_csv: output/lib/data_min_max_fu.csv
## ####################################
## subsequent vaccination
## ####################################
## plot cumulative incidence of subsequent vaccination
plot_cumulative_incidence:
run: r:latest analysis/subsequent_vax/plot_cumulative_incidence.R
needs:
- data_covariates_process
outputs:
moderately_sensitive:
ci_vax: output/subsequent_vax/images/ci_vax.png
survtable: output/subsequent_vax/tables/survtable_redacted.csv
## ####################################
## table 1 for report
## ####################################
## create table 1 for all and for each subgroup
table1:
run: r:latest analysis/report/table1.R
needs:
- data_eligible_ab
- data_eligible_cde
- data_covariates_process
outputs:
moderately_sensitive:
eligibility_count_p1: output/tables/eligibility_count_p1.csv
eligibility_count_all: output/tables/eligibility_count_all.csv
table_csv: output/report/tables/table1_*_REDACTED.csv
table_html: output/report/tables/table1_*_REDACTED.html
## ####################################
## process time to event data
## ####################################
## process tte data
data_tte_process_BNT162b2:
run: r:latest analysis/comparisons/data_tte_process.R BNT162b2
needs:
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_BNT162b2*.rds
moderately_sensitive:
event_counts_csv: output/tte/data/event_counts_BNT162b2.csv
event_counts_txt: output/tte/tables/event_counts_BNT162b2.txt
data_tte_process_ChAdOx1:
run: r:latest analysis/comparisons/data_tte_process.R ChAdOx1
needs:
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_ChAdOx1*.rds
moderately_sensitive:
event_counts_csv: output/tte/data/event_counts_ChAdOx1.csv
event_counts_txt: output/tte/tables/event_counts_ChAdOx1.txt
## check distribution of follow-up time in relation to variant dates
check_fu_1:
run: r:latest analysis/comparisons/check_fu.R 1
needs:
- data_covariates_process
- data_tte_process_BNT162b2
- data_tte_process_ChAdOx1
outputs:
moderately_sensitive:
check_fu_plot: output/tte/images/check_fu_1.png
check_fu_plot_data: output/tte/images/check_fu_1.csv
check_fu_2:
run: r:latest analysis/comparisons/check_fu.R 2
needs:
- data_covariates_process
- data_tte_process_BNT162b2
- data_tte_process_ChAdOx1
outputs:
moderately_sensitive:
check_fu_plot: output/tte/images/check_fu_2.png
check_fu_plot_data: output/tte/images/check_fu_2.csv
check_fu_3:
run: r:latest analysis/comparisons/check_fu.R 3
needs:
- data_covariates_process
- data_tte_process_BNT162b2
- data_tte_process_ChAdOx1
outputs:
moderately_sensitive:
check_fu_plot: output/tte/images/check_fu_3.png
check_fu_plot_data: output/tte/images/check_fu_3.csv
check_fu_4:
run: r:latest analysis/comparisons/check_fu.R 4
needs:
- data_covariates_process
- data_tte_process_BNT162b2
- data_tte_process_ChAdOx1
outputs:
moderately_sensitive:
check_fu_plot: output/tte/images/check_fu_4.png
check_fu_plot_data: output/tte/images/check_fu_4.csv
## ####################################
## apply models
## ####################################
## BNT162b2; 1; anytest
## preflight checks
preflight_BNT162b2_1_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 anytest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_anytest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_1_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 anytest
needs:
- preflight_BNT162b2_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_anytest.txt
## BNT162b2; 1; postest
## preflight checks
preflight_BNT162b2_1_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 postest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_postest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_1_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 postest
needs:
- preflight_BNT162b2_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_postest.txt
## BNT162b2; 1; covidadmitted
## preflight checks
preflight_BNT162b2_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidadmitted
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_covidadmitted*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_1_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 covidadmitted
needs:
- preflight_BNT162b2_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_covidadmitted.txt
## BNT162b2; 1; coviddeath
## preflight checks
preflight_BNT162b2_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 coviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_coviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_1_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 coviddeath
needs:
- preflight_BNT162b2_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_coviddeath.txt
## BNT162b2; 1; noncoviddeath
## preflight checks
preflight_BNT162b2_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 noncoviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_noncoviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_1_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 noncoviddeath
needs:
- preflight_BNT162b2_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_noncoviddeath.txt
## BNT162b2; 2; anytest
## preflight checks
preflight_BNT162b2_2_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 anytest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_anytest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_2_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 anytest
needs:
- preflight_BNT162b2_2_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_anytest.txt
## BNT162b2; 2; postest
## preflight checks
preflight_BNT162b2_2_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 postest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_postest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_2_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 postest
needs:
- preflight_BNT162b2_2_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_postest.txt
## BNT162b2; 2; covidadmitted
## preflight checks
preflight_BNT162b2_2_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidadmitted
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_covidadmitted*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_2_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 covidadmitted
needs:
- preflight_BNT162b2_2_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_covidadmitted.txt
## BNT162b2; 2; coviddeath
## preflight checks
preflight_BNT162b2_2_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 coviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_coviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_2_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 coviddeath
needs:
- preflight_BNT162b2_2_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_coviddeath.txt
## BNT162b2; 2; noncoviddeath
## preflight checks
preflight_BNT162b2_2_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 noncoviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_noncoviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_2_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 noncoviddeath
needs:
- preflight_BNT162b2_2_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_noncoviddeath.txt
## BNT162b2; 3; anytest
## preflight checks
preflight_BNT162b2_3_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 anytest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_anytest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_3_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 anytest
needs:
- preflight_BNT162b2_3_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_anytest.txt
## BNT162b2; 3; postest
## preflight checks
preflight_BNT162b2_3_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 postest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_postest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_3_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 postest
needs:
- preflight_BNT162b2_3_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_postest.txt
## BNT162b2; 3; covidadmitted
## preflight checks
preflight_BNT162b2_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidadmitted
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_covidadmitted*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_3_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 covidadmitted
needs:
- preflight_BNT162b2_3_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_covidadmitted.txt
## BNT162b2; 3; coviddeath
## preflight checks
preflight_BNT162b2_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 coviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_coviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_3_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 coviddeath
needs:
- preflight_BNT162b2_3_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_coviddeath.txt
## BNT162b2; 3; noncoviddeath
## preflight checks
preflight_BNT162b2_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 noncoviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_noncoviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_3_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 noncoviddeath
needs:
- preflight_BNT162b2_3_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_noncoviddeath.txt
## BNT162b2; 4; anytest
## preflight checks
preflight_BNT162b2_4_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 anytest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_anytest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_4_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 anytest
needs:
- preflight_BNT162b2_4_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_anytest.txt
## BNT162b2; 4; postest
## preflight checks
preflight_BNT162b2_4_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 postest
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_postest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_4_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 postest
needs:
- preflight_BNT162b2_4_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_postest.txt
## BNT162b2; 4; covidadmitted
## preflight checks
preflight_BNT162b2_4_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidadmitted
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_covidadmitted*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_4_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 covidadmitted
needs:
- preflight_BNT162b2_4_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_covidadmitted.txt
## BNT162b2; 4; coviddeath
## preflight checks
preflight_BNT162b2_4_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 coviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_coviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_4_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 coviddeath
needs:
- preflight_BNT162b2_4_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_coviddeath.txt
## BNT162b2; 4; noncoviddeath
## preflight checks
preflight_BNT162b2_4_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 noncoviddeath
needs:
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_noncoviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_4_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 noncoviddeath
needs:
- preflight_BNT162b2_4_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_noncoviddeath.txt
## ChAdOx1; 1; anytest
## preflight checks
preflight_ChAdOx1_1_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 anytest
needs:
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_anytest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_anytest*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 anytest
needs:
- preflight_ChAdOx1_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_anytest.txt
## ChAdOx1; 1; postest
## preflight checks
preflight_ChAdOx1_1_postest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 postest
needs:
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_postest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_postest*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 postest
needs:
- preflight_ChAdOx1_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_postest.txt
## ChAdOx1; 1; covidadmitted
## preflight checks
preflight_ChAdOx1_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 covidadmitted
needs:
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_covidadmitted*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_covidadmitted*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 covidadmitted
needs:
- preflight_ChAdOx1_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_covidadmitted.txt
## ChAdOx1; 1; coviddeath
## preflight checks
preflight_ChAdOx1_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 coviddeath
needs:
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_coviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_coviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 coviddeath
needs:
- preflight_ChAdOx1_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_coviddeath.txt
## ChAdOx1; 1; noncoviddeath
## preflight checks
preflight_ChAdOx1_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 noncoviddeath
needs:
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_noncoviddeath*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_noncoviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 noncoviddeath
needs:
- preflight_ChAdOx1_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_noncoviddeath.txt
## ChAdOx1; 2; anytest
## preflight checks
preflight_ChAdOx1_2_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 anytest
needs:
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_2_anytest*.rds
moderately_sensitive:
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_anytest*.txt
## apply cox model
apply_model_cox_ChAdOx1_2_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 anytest
needs:
- preflight_ChAdOx1_2_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_2_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_anytest*.rds