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project.yaml
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version: '3.0'
expectations:
population_size: 100000
actions:
## ####################################
## 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:
run: r:latest analysis/dummy_data.R
needs:
- design
outputs:
moderately_sensitive:
dummy_data: analysis/dummy_data.feather
## study definition
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition
--output-format feather
dummy_data_file: analysis/dummy_data.feather
needs:
- design
- dummy_data
outputs:
highly_sensitive:
cohort: output/input.feather
## ####################################
## preprocessing
## ####################################
## process data from study_definition
data_input_process:
run: r:latest analysis/preprocess/data_input_process.R
needs:
- design
- dummy_data
- generate_study_population
outputs:
highly_sensitive:
data_wide_vax_dates: output/data/data_wide_vax_dates.rds
data_long_shielded_dates: output/data/data_long_shielded_dates.rds
data_long_nonshielded_dates: output/data/data_long_nonshielded_dates.rds
data_long_bmi_dates: output/data/data_long_bmi_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/second_vax_period/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 tests
## ####################################
## generate dummy data for study_definition_tests
dummy_data_tests:
run: r:latest analysis/dummy_data_tests.R
needs:
- design
- dummy_data
- data_eligible_cde
outputs:
moderately_sensitive:
dummy_data_tests: analysis/dummy_data_tests.feather
## study definition tests
generate_covid_tests_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_tests
--output-format feather
dummy_data_file: analysis/dummy_data_tests.feather
needs:
- design
- data_eligible_cde
- dummy_data_tests
outputs:
highly_sensitive:
cohort: output/input_tests.feather
## check the tests data as expected and save processed data
process_tests:
run: r:latest analysis/tests/process_tests.R
needs:
- design
- data_input_process
- data_eligible_cde
- generate_covid_tests_data
outputs:
highly_sensitive:
data_tests: output/data/data_tests.rds
data_pregnancy: output/data/data_pregnancy.rds
moderately_sensitive:
pos_rate_distribution: output/tests/images/pos_rate_distribution.png
## ####################################
## 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
- process_tests
outputs:
moderately_sensitive:
table_csv: output/report/tables/table1_*_REDACTED.csv
table_html: output/report/tables/table1_*_REDACTED.html
## ####################################
## comparisons
## ####################################
## process comparisons data
data_comparisons_process:
run: r:latest analysis/comparisons/data_comparisons_process.R
needs:
- design
- data_input_process
- data_2nd_vax_dates
- data_eligible_cde
- process_tests
outputs:
highly_sensitive:
data_comparisons: output/comparisons/data/data_comparisons_*.rds
## process tte data
data_tte_process_BNT162b2:
run: r:latest analysis/comparisons/data_tte_process.R BNT162b2
needs:
- design
- data_input_process
- data_comparisons_process
- process_tests
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_comparisons_process
- process_tests
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_comparisons_process
- process_tests
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 and clinically vulnerable; anytest
## preflight checks
preflight_BNT162b2_1_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 anytest
needs:
- design
- data_comparisons_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 and clinically vulnerable; postest
## preflight checks
preflight_BNT162b2_1_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 postest
needs:
- design
- data_comparisons_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 and clinically vulnerable; covidadmitted
## preflight checks
preflight_BNT162b2_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidadmitted
needs:
- design
- data_comparisons_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 and clinically vulnerable; coviddeath
## preflight checks
preflight_BNT162b2_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 coviddeath
needs:
- design
- data_comparisons_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 and clinically vulnerable; noncoviddeath
## preflight checks
preflight_BNT162b2_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 noncoviddeath
needs:
- design
- data_comparisons_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; anytest
## preflight checks
preflight_BNT162b2_2_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 anytest
needs:
- design
- data_comparisons_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; postest
## preflight checks
preflight_BNT162b2_2_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 postest
needs:
- design
- data_comparisons_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; covidadmitted
## preflight checks
preflight_BNT162b2_2_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidadmitted
needs:
- design
- data_comparisons_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; coviddeath
## preflight checks
preflight_BNT162b2_2_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 coviddeath
needs:
- design
- data_comparisons_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; noncoviddeath
## preflight checks
preflight_BNT162b2_2_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 noncoviddeath
needs:
- design
- data_comparisons_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_coviddeath
- 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; anytest
## preflight checks
preflight_BNT162b2_3_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 anytest
needs:
- design
- data_comparisons_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; postest
## preflight checks
preflight_BNT162b2_3_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 postest
needs:
- design
- data_comparisons_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; covidadmitted
## preflight checks
preflight_BNT162b2_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidadmitted
needs:
- design
- data_comparisons_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; coviddeath
## preflight checks
preflight_BNT162b2_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 coviddeath
needs:
- design
- data_comparisons_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; noncoviddeath
## preflight checks
preflight_BNT162b2_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 noncoviddeath
needs:
- design
- data_comparisons_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+; anytest
## preflight checks
preflight_BNT162b2_4_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 anytest
needs:
- design
- data_comparisons_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+; postest
## preflight checks
preflight_BNT162b2_4_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 postest
needs:
- design
- data_comparisons_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+; covidadmitted
## preflight checks
preflight_BNT162b2_4_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidadmitted
needs:
- design
- data_comparisons_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+; coviddeath
## preflight checks
preflight_BNT162b2_4_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 coviddeath
needs:
- design
- data_comparisons_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+; noncoviddeath
## preflight checks
preflight_BNT162b2_4_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 noncoviddeath
needs:
- design
- data_comparisons_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:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_BNT162b2_4.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_BNT162b2_4.txt
## ChAdOx; 16-64 and clinically vulnerable; anytest
## preflight checks
preflight_ChAdOx_1_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx 1 anytest
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_1_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_anytest_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_anytest.txt
## apply cox model
apply_model_cox_ChAdOx_1_anytest:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 anytest
needs:
- design
- preflight_ChAdOx_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_1_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_anytest.rds
## ChAdOx; 16-64 and clinically vulnerable; postest
## preflight checks
preflight_ChAdOx_1_postest:
run: r:latest analysis/comparisons/preflight.R ChAdOx 1 postest
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_1_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_postest_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_postest.txt
## apply cox model
apply_model_cox_ChAdOx_1_postest:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 postest
needs:
- design
- preflight_ChAdOx_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_1_postest.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_postest.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_postest.rds
## ChAdOx; 16-64 and clinically vulnerable; covidadmitted
## preflight checks
preflight_ChAdOx_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R ChAdOx 1 covidadmitted
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs: