generated from opensafely/research-template
/
project.yaml
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/
project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml or study_definition_1-6.py DIRECTLY
## These files are created by create-project.R
## Edit and run create-project.R to update the project.yaml
## Edit study_definition_k.py and run create-project.R to update
## study_definition_1-6.py
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## ####################################
## preliminaries
## ####################################
design:
run: r:latest analysis/design.R
outputs:
moderately_sensitive:
study_dates_json: output/lib/study_parameters.json
study_dates_rds: output/lib/study_parameters.rds
jcvi_groups: output/lib/jcvi_groups.csv
elig_dates: output/lib/elig_dates.csv
regions: output/lib/regions.csv
model_varlist: output/lib/model_varlist.rds
outcomes: output/lib/outcomes.rds
strata_vars: output/lib/strata_vars.rds
subgroups: output/lib/subgroups.rds
## ####################################
## study definition
## ####################################
## generate dummy data for study_definition
dummy_data_vax:
run: r:latest analysis/dummy_data_vax.R
needs:
- design
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:
- design
- 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:
- design
- 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:
- design
- 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: output/tables/eligibility_count_ab.txt
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:
- design
- 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:
- design
- data_eligible_ab
- data_2nd_vax_dates
outputs:
moderately_sensitive:
plots_by_region: output/second_vax_period/images/plot_by_region_*.png
## apply eligiblity criteria from boxes c, d and e
data_eligible_cde:
run: r:latest analysis/preprocess/data_eligible_cde.R
needs:
- design
- 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
## ####################################
## study definition ever and k
## ####################################
## study definition ever
generate_ever_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ever
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_ever.feather
## study definition for period 1
generate_input_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_1
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_1.feather
## study definition for period 2
generate_input_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_2.feather
## study definition for period 3
generate_input_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_3
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_3.feather
## study definition for period 4
generate_input_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_4
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_4.feather
## study definition for period 5
generate_input_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_5
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_5.feather
## study definition for period 6
generate_input_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_6
--output-format feather
needs:
- design
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_6.feather
## ####################################
## process covariates data
## ####################################
## (includes anytest_date)
data_covariates_process:
run: r:latest analysis/preprocess/data_covariates_process.R
needs:
- design
- data_input_process
- data_eligible_cde
- generate_ever_data
- generate_input_1
- generate_input_2
- generate_input_3
- generate_input_4
- generate_input_5
- generate_input_6
outputs:
highly_sensitive:
data_covariates: output/data/data_covariates.rds
## ####################################
## subsequent vaccination
## ####################################
## plot cumulative incidence of subsequent vaccination
plot_cumulative_incidence:
run: r:latest analysis/subsequent_vax/plot_cumulative_incidence.R
needs:
- design
- data_input_process
- data_eligible_cde
outputs:
moderately_sensitive:
ci_vax: output/subsequent_vax/images/ci_vax_*.png
survtable: output/subsequent_vax/tables/survtable_*.txt
## ####################################
## table 1 for report
## ####################################
## create table 1 for all and for each subgroup
table1:
run: r:latest analysis/report/table1.R
needs:
- design
- data_input_process
- data_eligible_cde
- data_covariates_process
outputs:
moderately_sensitive:
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:
- design
- data_input_process
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_BNT162b2*.rds
event_counts: output/tte/tables/event_counts_BNT162b2.rds
data_tte_process_ChAdOx:
run: r:latest analysis/comparisons/data_tte_process.R ChAdOx
needs:
- design
- data_input_process
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_ChAdOx*.rds
event_counts: output/tte/tables/event_counts_ChAdOx.rds
data_tte_process_both:
run: r:latest analysis/comparisons/data_tte_process.R both
needs:
- design
- data_input_process
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_both*.rds
event_counts: output/tte/tables/event_counts_both.rds
## process event counts tables
process_event_count_tables:
run: r:latest analysis/comparisons/process_event_count_tables.R
needs:
- design
- data_tte_process_BNT162b2
- data_tte_process_ChAdOx
outputs:
moderately_sensitive:
tidy_tables_events: output/tte/tables/tidy_events*.txt
## ####################################
## apply models
## ####################################
## BNT162b2; 16-64 years and clinically vulnerable; anytest
## preflight checks
preflight_BNT162b2_1_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 anytest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_anytest_*.html
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.R BNT162b2 1 anytest
needs:
- design
- preflight_BNT162b2_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_anytest.rds
## BNT162b2; 16-64 years and clinically vulnerable; postest
## preflight checks
preflight_BNT162b2_1_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 postest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_postest_*.html
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.R BNT162b2 1 postest
needs:
- design
- preflight_BNT162b2_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_postest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_postest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_postest.rds
## BNT162b2; 16-64 years and clinically vulnerable; covidadmitted
## preflight checks
preflight_BNT162b2_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidadmitted
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_covidadmitted_*.html
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.R BNT162b2 1 covidadmitted
needs:
- design
- preflight_BNT162b2_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_covidadmitted.rds
## BNT162b2; 16-64 years and clinically vulnerable; coviddeath
## preflight checks
preflight_BNT162b2_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 coviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_coviddeath_*.html
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.R BNT162b2 1 coviddeath
needs:
- design
- preflight_BNT162b2_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_coviddeath.rds
## BNT162b2; 16-64 years and clinically vulnerable; noncoviddeath
## preflight checks
preflight_BNT162b2_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 noncoviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_noncoviddeath_*.html
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.R BNT162b2 1 noncoviddeath
needs:
- design
- preflight_BNT162b2_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_1_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_1_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_BNT162b2_1:
run: r:latest analysis/comparisons/tables_cox.R BNT162b2 1
needs:
- design
- data_2nd_vax_dates
- data_tte_process_BNT162b2
- apply_model_cox_BNT162b2_1_anytest
- apply_model_cox_BNT162b2_1_postest
- apply_model_cox_BNT162b2_1_covidadmitted
- apply_model_cox_BNT162b2_1_coviddeath
- apply_model_cox_BNT162b2_1_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_1.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_1.txt
## BNT162b2; 18-39 years; anytest
## preflight checks
preflight_BNT162b2_2_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 anytest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_anytest_*.html
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.R BNT162b2 2 anytest
needs:
- design
- preflight_BNT162b2_2_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_anytest.rds
## BNT162b2; 18-39 years; postest
## preflight checks
preflight_BNT162b2_2_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 postest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_postest_*.html
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.R BNT162b2 2 postest
needs:
- design
- preflight_BNT162b2_2_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_postest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_postest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_postest.rds
## BNT162b2; 18-39 years; covidadmitted
## preflight checks
preflight_BNT162b2_2_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidadmitted
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_covidadmitted_*.html
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.R BNT162b2 2 covidadmitted
needs:
- design
- preflight_BNT162b2_2_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_covidadmitted.rds
## BNT162b2; 18-39 years; coviddeath
## preflight checks
preflight_BNT162b2_2_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 coviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_coviddeath_*.html
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.R BNT162b2 2 coviddeath
needs:
- design
- preflight_BNT162b2_2_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_coviddeath.rds
## BNT162b2; 18-39 years; noncoviddeath
## preflight checks
preflight_BNT162b2_2_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 noncoviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_noncoviddeath_*.html
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.R BNT162b2 2 noncoviddeath
needs:
- design
- preflight_BNT162b2_2_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_2_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_2_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_BNT162b2_2:
run: r:latest analysis/comparisons/tables_cox.R BNT162b2 2
needs:
- design
- data_2nd_vax_dates
- data_tte_process_BNT162b2
- apply_model_cox_BNT162b2_2_anytest
- apply_model_cox_BNT162b2_2_postest
- apply_model_cox_BNT162b2_2_covidadmitted
- apply_model_cox_BNT162b2_2_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_2.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_2.txt
## BNT162b2; 40-64 years; anytest
## preflight checks
preflight_BNT162b2_3_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 anytest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_anytest_*.html
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.R BNT162b2 3 anytest
needs:
- design
- preflight_BNT162b2_3_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_anytest.rds
## BNT162b2; 40-64 years; postest
## preflight checks
preflight_BNT162b2_3_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 postest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_postest_*.html
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.R BNT162b2 3 postest
needs:
- design
- preflight_BNT162b2_3_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_postest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_postest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_postest.rds
## BNT162b2; 40-64 years; covidadmitted
## preflight checks
preflight_BNT162b2_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidadmitted
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_covidadmitted_*.html
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.R BNT162b2 3 covidadmitted
needs:
- design
- preflight_BNT162b2_3_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_covidadmitted.rds
## BNT162b2; 40-64 years; coviddeath
## preflight checks
preflight_BNT162b2_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 coviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_coviddeath_*.html
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.R BNT162b2 3 coviddeath
needs:
- design
- preflight_BNT162b2_3_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_coviddeath.rds
## BNT162b2; 40-64 years; noncoviddeath
## preflight checks
preflight_BNT162b2_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 noncoviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_noncoviddeath_*.html
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.R BNT162b2 3 noncoviddeath
needs:
- design
- preflight_BNT162b2_3_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_3_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_3_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_BNT162b2_3:
run: r:latest analysis/comparisons/tables_cox.R BNT162b2 3
needs:
- design
- data_2nd_vax_dates
- data_tte_process_BNT162b2
- apply_model_cox_BNT162b2_3_anytest
- apply_model_cox_BNT162b2_3_postest
- apply_model_cox_BNT162b2_3_covidadmitted
- apply_model_cox_BNT162b2_3_coviddeath
- apply_model_cox_BNT162b2_3_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_3.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_3.txt
## BNT162b2; 65+ years; anytest
## preflight checks
preflight_BNT162b2_4_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 anytest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_anytest_*.html
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.R BNT162b2 4 anytest
needs:
- design
- preflight_BNT162b2_4_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_anytest.rds
## BNT162b2; 65+ years; postest
## preflight checks
preflight_BNT162b2_4_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 postest
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_postest_*.html
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.R BNT162b2 4 postest
needs:
- design
- preflight_BNT162b2_4_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_postest.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_postest.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_postest.rds
## BNT162b2; 65+ years; covidadmitted
## preflight checks
preflight_BNT162b2_4_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidadmitted
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_covidadmitted_*.html
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.R BNT162b2 4 covidadmitted
needs:
- design
- preflight_BNT162b2_4_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_covidadmitted.rds
## BNT162b2; 65+ years; coviddeath
## preflight checks
preflight_BNT162b2_4_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 coviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_coviddeath_*.html
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.R BNT162b2 4 coviddeath
needs:
- design
- preflight_BNT162b2_4_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_coviddeath.rds
## BNT162b2; 65+ years; noncoviddeath
## preflight checks
preflight_BNT162b2_4_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 noncoviddeath
needs:
- design
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_noncoviddeath_*.html
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.R BNT162b2 4 noncoviddeath
needs:
- design
- preflight_BNT162b2_4_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_BNT162b2_4_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_BNT162b2_4_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_BNT162b2_4:
run: r:latest analysis/comparisons/tables_cox.R BNT162b2 4
needs:
- design
- data_2nd_vax_dates
- data_tte_process_BNT162b2
- apply_model_cox_BNT162b2_4_anytest
- apply_model_cox_BNT162b2_4_postest
- apply_model_cox_BNT162b2_4_covidadmitted
- apply_model_cox_BNT162b2_4_coviddeath
- apply_model_cox_BNT162b2_4_noncoviddeath
outputs: