Job request: 5324
- Organisation:
- University of Bristol
- Workspace:
- covid-ve-change-over-time-main
- ID:
- 2wyb3codke2drmd4
This page shows the technical details of what happened when authorised researcher Elsie Horne requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the indicated Requested Actions with the
Pipeline section below, you can infer what
security level
various outputs were written to. Outputs marked as
highly_sensitive
can never be viewed directly by a researcher; they can only
request that code runs against them. Outputs marked as
moderately_sensitive
can be viewed by an approved researcher by logging into a highly
secure environment. Only outputs marked as
moderately_sensitive
can be requested for release to the public, via a controlled
output review service.
Jobs
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Pipeline
Show project.yaml
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
data_age: output/data/data_age.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 years 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 years 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 years 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 years 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 years 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 years; 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 years; 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 years; 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 years; 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 years; 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_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_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 years; 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 years; 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 years; 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 years; 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+ years; 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+ years; 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+ years; 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+ years; 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+ years; 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 years 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 years 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 years 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:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_1_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_covidadmitted_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_covidadmitted.txt
## apply cox model
apply_model_cox_ChAdOx_1_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 covidadmitted
needs:
- design
- preflight_ChAdOx_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_1_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_covidadmitted.rds
## ChAdOx; 16-64 years and clinically vulnerable; coviddeath
## preflight checks
preflight_ChAdOx_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx 1 coviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_1_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_coviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_coviddeath.txt
## apply cox model
apply_model_cox_ChAdOx_1_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 coviddeath
needs:
- design
- preflight_ChAdOx_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_1_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_coviddeath.rds
## ChAdOx; 16-64 years and clinically vulnerable; noncoviddeath
## preflight checks
preflight_ChAdOx_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx 1 noncoviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_1_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_1_noncoviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_1_noncoviddeath.txt
## apply cox model
apply_model_cox_ChAdOx_1_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 1 noncoviddeath
needs:
- design
- preflight_ChAdOx_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_1_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_1_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_1_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_ChAdOx_1:
run: r:latest analysis/comparisons/tables_cox.R ChAdOx 1
needs:
- design
- data_2nd_vax_dates
- data_tte_process_ChAdOx
- apply_model_cox_ChAdOx_1_anytest
- apply_model_cox_ChAdOx_1_postest
- apply_model_cox_ChAdOx_1_covidadmitted
- apply_model_cox_ChAdOx_1_coviddeath
- apply_model_cox_ChAdOx_1_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_ChAdOx_1.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_ChAdOx_1.txt
## ChAdOx; 40-64 years; anytest
## preflight checks
preflight_ChAdOx_3_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx 3 anytest
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_3_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_anytest_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_anytest.txt
## apply cox model
apply_model_cox_ChAdOx_3_anytest:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 anytest
needs:
- design
- preflight_ChAdOx_3_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_3_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_anytest.rds
## ChAdOx; 40-64 years; postest
## preflight checks
preflight_ChAdOx_3_postest:
run: r:latest analysis/comparisons/preflight.R ChAdOx 3 postest
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_3_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_postest_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_postest.txt
## apply cox model
apply_model_cox_ChAdOx_3_postest:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 postest
needs:
- design
- preflight_ChAdOx_3_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_3_postest.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_postest.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_postest.rds
## ChAdOx; 40-64 years; covidadmitted
## preflight checks
preflight_ChAdOx_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R ChAdOx 3 covidadmitted
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_3_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_covidadmitted_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_covidadmitted.txt
## apply cox model
apply_model_cox_ChAdOx_3_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 covidadmitted
needs:
- design
- preflight_ChAdOx_3_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_3_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_covidadmitted.rds
## ChAdOx; 40-64 years; coviddeath
## preflight checks
preflight_ChAdOx_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx 3 coviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_3_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_coviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_coviddeath.txt
## apply cox model
apply_model_cox_ChAdOx_3_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 coviddeath
needs:
- design
- preflight_ChAdOx_3_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_3_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_coviddeath.rds
## ChAdOx; 40-64 years; noncoviddeath
## preflight checks
preflight_ChAdOx_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx 3 noncoviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_3_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_3_noncoviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_3_noncoviddeath.txt
## apply cox model
apply_model_cox_ChAdOx_3_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 3 noncoviddeath
needs:
- design
- preflight_ChAdOx_3_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_3_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_3_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_3_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_ChAdOx_3:
run: r:latest analysis/comparisons/tables_cox.R ChAdOx 3
needs:
- design
- data_2nd_vax_dates
- data_tte_process_ChAdOx
- apply_model_cox_ChAdOx_3_anytest
- apply_model_cox_ChAdOx_3_postest
- apply_model_cox_ChAdOx_3_covidadmitted
- apply_model_cox_ChAdOx_3_coviddeath
- apply_model_cox_ChAdOx_3_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_ChAdOx_3.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_ChAdOx_3.txt
## ChAdOx; 65+ years; anytest
## preflight checks
preflight_ChAdOx_4_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx 4 anytest
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_4_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_anytest_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_anytest.txt
## apply cox model
apply_model_cox_ChAdOx_4_anytest:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 anytest
needs:
- design
- preflight_ChAdOx_4_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_4_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_anytest.rds
## ChAdOx; 65+ years; postest
## preflight checks
preflight_ChAdOx_4_postest:
run: r:latest analysis/comparisons/preflight.R ChAdOx 4 postest
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_4_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_postest_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_postest.txt
## apply cox model
apply_model_cox_ChAdOx_4_postest:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 postest
needs:
- design
- preflight_ChAdOx_4_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_4_postest.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_postest.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_postest.rds
## ChAdOx; 65+ years; covidadmitted
## preflight checks
preflight_ChAdOx_4_covidadmitted:
run: r:latest analysis/comparisons/preflight.R ChAdOx 4 covidadmitted
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_4_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_covidadmitted_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_covidadmitted.txt
## apply cox model
apply_model_cox_ChAdOx_4_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 covidadmitted
needs:
- design
- preflight_ChAdOx_4_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_4_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_covidadmitted.rds
## ChAdOx; 65+ years; coviddeath
## preflight checks
preflight_ChAdOx_4_coviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx 4 coviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_4_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_coviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_coviddeath.txt
## apply cox model
apply_model_cox_ChAdOx_4_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 coviddeath
needs:
- design
- preflight_ChAdOx_4_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_4_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_coviddeath.rds
## ChAdOx; 65+ years; noncoviddeath
## preflight checks
preflight_ChAdOx_4_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx 4 noncoviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_ChAdOx
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx_4_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx_4_noncoviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx_4_noncoviddeath.txt
## apply cox model
apply_model_cox_ChAdOx_4_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R ChAdOx 4 noncoviddeath
needs:
- design
- preflight_ChAdOx_4_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx_4_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_ChAdOx_4_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_ChAdOx_4_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_ChAdOx_4:
run: r:latest analysis/comparisons/tables_cox.R ChAdOx 4
needs:
- design
- data_2nd_vax_dates
- data_tte_process_ChAdOx
- apply_model_cox_ChAdOx_4_anytest
- apply_model_cox_ChAdOx_4_postest
- apply_model_cox_ChAdOx_4_covidadmitted
- apply_model_cox_ChAdOx_4_coviddeath
- apply_model_cox_ChAdOx_4_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_ChAdOx_4.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_ChAdOx_4.txt
## both; 16-64 years and clinically vulnerable; anytest
## preflight checks
preflight_both_1_anytest:
run: r:latest analysis/comparisons/preflight.R both 1 anytest
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_1_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_1_anytest_*.html
preflight_report: output/preflight/tables/preflight_report_both_1_anytest.txt
## apply cox model
apply_model_cox_both_1_anytest:
run: r:latest analysis/comparisons/apply_model_cox.R both 1 anytest
needs:
- design
- preflight_both_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_both_1_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_both_1_anytest.rds
## both; 16-64 years and clinically vulnerable; postest
## preflight checks
preflight_both_1_postest:
run: r:latest analysis/comparisons/preflight.R both 1 postest
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_1_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_1_postest_*.html
preflight_report: output/preflight/tables/preflight_report_both_1_postest.txt
## apply cox model
apply_model_cox_both_1_postest:
run: r:latest analysis/comparisons/apply_model_cox.R both 1 postest
needs:
- design
- preflight_both_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_postest.rds
model_summary: output/models_cox/data/modelcox_summary_both_1_postest.rds
model_glance: output/models_cox/data/modelcox_glance_both_1_postest.rds
## both; 16-64 years and clinically vulnerable; covidadmitted
## preflight checks
preflight_both_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R both 1 covidadmitted
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_1_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_1_covidadmitted_*.html
preflight_report: output/preflight/tables/preflight_report_both_1_covidadmitted.txt
## apply cox model
apply_model_cox_both_1_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox.R both 1 covidadmitted
needs:
- design
- preflight_both_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_both_1_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_both_1_covidadmitted.rds
## both; 16-64 years and clinically vulnerable; coviddeath
## preflight checks
preflight_both_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R both 1 coviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_1_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_1_coviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_both_1_coviddeath.txt
## apply cox model
apply_model_cox_both_1_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R both 1 coviddeath
needs:
- design
- preflight_both_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_both_1_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_both_1_coviddeath.rds
## both; 16-64 years and clinically vulnerable; noncoviddeath
## preflight checks
preflight_both_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R both 1 noncoviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_1_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_1_noncoviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_both_1_noncoviddeath.txt
## apply cox model
apply_model_cox_both_1_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R both 1 noncoviddeath
needs:
- design
- preflight_both_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_both_1_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_both_1_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_both_1:
run: r:latest analysis/comparisons/tables_cox.R both 1
needs:
- design
- data_2nd_vax_dates
- data_tte_process_both
- apply_model_cox_both_1_anytest
- apply_model_cox_both_1_postest
- apply_model_cox_both_1_covidadmitted
- apply_model_cox_both_1_coviddeath
- apply_model_cox_both_1_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_both_1.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_both_1.txt
## both; 40-64 years; anytest
## preflight checks
preflight_both_3_anytest:
run: r:latest analysis/comparisons/preflight.R both 3 anytest
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_3_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_3_anytest_*.html
preflight_report: output/preflight/tables/preflight_report_both_3_anytest.txt
## apply cox model
apply_model_cox_both_3_anytest:
run: r:latest analysis/comparisons/apply_model_cox.R both 3 anytest
needs:
- design
- preflight_both_3_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_both_3_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_both_3_anytest.rds
## both; 40-64 years; postest
## preflight checks
preflight_both_3_postest:
run: r:latest analysis/comparisons/preflight.R both 3 postest
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_3_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_3_postest_*.html
preflight_report: output/preflight/tables/preflight_report_both_3_postest.txt
## apply cox model
apply_model_cox_both_3_postest:
run: r:latest analysis/comparisons/apply_model_cox.R both 3 postest
needs:
- design
- preflight_both_3_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_postest.rds
model_summary: output/models_cox/data/modelcox_summary_both_3_postest.rds
model_glance: output/models_cox/data/modelcox_glance_both_3_postest.rds
## both; 40-64 years; covidadmitted
## preflight checks
preflight_both_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R both 3 covidadmitted
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_3_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_3_covidadmitted_*.html
preflight_report: output/preflight/tables/preflight_report_both_3_covidadmitted.txt
## apply cox model
apply_model_cox_both_3_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox.R both 3 covidadmitted
needs:
- design
- preflight_both_3_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_both_3_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_both_3_covidadmitted.rds
## both; 40-64 years; coviddeath
## preflight checks
preflight_both_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R both 3 coviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_3_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_3_coviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_both_3_coviddeath.txt
## apply cox model
apply_model_cox_both_3_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R both 3 coviddeath
needs:
- design
- preflight_both_3_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_both_3_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_both_3_coviddeath.rds
## both; 40-64 years; noncoviddeath
## preflight checks
preflight_both_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R both 3 noncoviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_3_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_3_noncoviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_both_3_noncoviddeath.txt
## apply cox model
apply_model_cox_both_3_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R both 3 noncoviddeath
needs:
- design
- preflight_both_3_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_both_3_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_both_3_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_both_3:
run: r:latest analysis/comparisons/tables_cox.R both 3
needs:
- design
- data_2nd_vax_dates
- data_tte_process_both
- apply_model_cox_both_3_anytest
- apply_model_cox_both_3_postest
- apply_model_cox_both_3_covidadmitted
- apply_model_cox_both_3_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_both_3.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_both_3.txt
## both; 65+ years; anytest
## preflight checks
preflight_both_4_anytest:
run: r:latest analysis/comparisons/preflight.R both 4 anytest
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_4_anytest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_4_anytest_*.html
preflight_report: output/preflight/tables/preflight_report_both_4_anytest.txt
## apply cox model
apply_model_cox_both_4_anytest:
run: r:latest analysis/comparisons/apply_model_cox.R both 4 anytest
needs:
- design
- preflight_both_4_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_4_anytest.rds
model_summary: output/models_cox/data/modelcox_summary_both_4_anytest.rds
model_glance: output/models_cox/data/modelcox_glance_both_4_anytest.rds
## both; 65+ years; postest
## preflight checks
preflight_both_4_postest:
run: r:latest analysis/comparisons/preflight.R both 4 postest
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_4_postest.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_4_postest_*.html
preflight_report: output/preflight/tables/preflight_report_both_4_postest.txt
## apply cox model
apply_model_cox_both_4_postest:
run: r:latest analysis/comparisons/apply_model_cox.R both 4 postest
needs:
- design
- preflight_both_4_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_4_postest.rds
model_summary: output/models_cox/data/modelcox_summary_both_4_postest.rds
model_glance: output/models_cox/data/modelcox_glance_both_4_postest.rds
## both; 65+ years; covidadmitted
## preflight checks
preflight_both_4_covidadmitted:
run: r:latest analysis/comparisons/preflight.R both 4 covidadmitted
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_4_covidadmitted.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_4_covidadmitted_*.html
preflight_report: output/preflight/tables/preflight_report_both_4_covidadmitted.txt
## apply cox model
apply_model_cox_both_4_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox.R both 4 covidadmitted
needs:
- design
- preflight_both_4_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_4_covidadmitted.rds
model_summary: output/models_cox/data/modelcox_summary_both_4_covidadmitted.rds
model_glance: output/models_cox/data/modelcox_glance_both_4_covidadmitted.rds
## both; 65+ years; coviddeath
## preflight checks
preflight_both_4_coviddeath:
run: r:latest analysis/comparisons/preflight.R both 4 coviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_4_coviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_4_coviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_both_4_coviddeath.txt
## apply cox model
apply_model_cox_both_4_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R both 4 coviddeath
needs:
- design
- preflight_both_4_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_4_coviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_both_4_coviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_both_4_coviddeath.rds
## both; 65+ years; noncoviddeath
## preflight checks
preflight_both_4_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R both 4 noncoviddeath
needs:
- design
- data_comparisons_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_4_noncoviddeath.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_4_noncoviddeath_*.html
preflight_report: output/preflight/tables/preflight_report_both_4_noncoviddeath.txt
## apply cox model
apply_model_cox_both_4_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox.R both 4 noncoviddeath
needs:
- design
- preflight_both_4_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_4_noncoviddeath.rds
model_summary: output/models_cox/data/modelcox_summary_both_4_noncoviddeath.rds
model_glance: output/models_cox/data/modelcox_glance_both_4_noncoviddeath.rds
## tabulate cox model for all outcomes
tables_model_cox_both_4:
run: r:latest analysis/comparisons/tables_cox.R both 4
needs:
- design
- data_2nd_vax_dates
- data_tte_process_both
- apply_model_cox_both_4_anytest
- apply_model_cox_both_4_postest
- apply_model_cox_both_4_covidadmitted
- apply_model_cox_both_4_coviddeath
- apply_model_cox_both_4_noncoviddeath
outputs:
moderately_sensitive:
table_glance: output/models_cox/tables/modelcox_glance_both_4.txt
table_coefficients: output/models_cox/tables/modelcox_coefficients_both_4.txt
## generate plots
## plot anytest BNT162b2
plot_hr_anytest_BNT162b2:
run: r:latest analysis/comparisons/plot_cox_anytest.R BNT162b2
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_BNT162b2_1_anytest
- apply_model_cox_BNT162b2_2_anytest
- apply_model_cox_BNT162b2_3_anytest
- apply_model_cox_BNT162b2_4_anytest
outputs:
moderately_sensitive:
plot: output/models_cox/images/hr_anytest_BNT162b2_*.png
## plot other outcomes BNT162b2
plot_hr_BNT162b2:
run: r:latest analysis/comparisons/plot_cox.R BNT162b2
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_BNT162b2_1_postest
- apply_model_cox_BNT162b2_1_covidadmitted
- apply_model_cox_BNT162b2_1_coviddeath
- apply_model_cox_BNT162b2_1_noncoviddeath
- apply_model_cox_BNT162b2_2_postest
- apply_model_cox_BNT162b2_2_covidadmitted
- apply_model_cox_BNT162b2_2_noncoviddeath
- apply_model_cox_BNT162b2_3_postest
- apply_model_cox_BNT162b2_3_covidadmitted
- apply_model_cox_BNT162b2_3_coviddeath
- apply_model_cox_BNT162b2_3_noncoviddeath
- 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:
plot: output/models_cox/images/hr_BNT162b2_*.png
## plot anytest ChAdOx
plot_hr_anytest_ChAdOx:
run: r:latest analysis/comparisons/plot_cox_anytest.R ChAdOx
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_ChAdOx_1_anytest
- apply_model_cox_ChAdOx_3_anytest
- apply_model_cox_ChAdOx_4_anytest
outputs:
moderately_sensitive:
plot: output/models_cox/images/hr_anytest_ChAdOx_*.png
## plot other outcomes ChAdOx
plot_hr_ChAdOx:
run: r:latest analysis/comparisons/plot_cox.R ChAdOx
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_ChAdOx_1_postest
- apply_model_cox_ChAdOx_1_covidadmitted
- apply_model_cox_ChAdOx_1_coviddeath
- apply_model_cox_ChAdOx_1_noncoviddeath
- apply_model_cox_ChAdOx_3_postest
- apply_model_cox_ChAdOx_3_covidadmitted
- apply_model_cox_ChAdOx_3_coviddeath
- apply_model_cox_ChAdOx_3_noncoviddeath
- apply_model_cox_ChAdOx_4_postest
- apply_model_cox_ChAdOx_4_covidadmitted
- apply_model_cox_ChAdOx_4_coviddeath
- apply_model_cox_ChAdOx_4_noncoviddeath
outputs:
moderately_sensitive:
plot: output/models_cox/images/hr_ChAdOx_*.png
## plot anytest BNT162b2andChAdOx
plot_hr_anytest_BNT162b2andChAdOx:
run: r:latest analysis/comparisons/plot_cox_anytest.R BNT162b2andChAdOx
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_BNT162b2_1_anytest
- apply_model_cox_BNT162b2_3_anytest
- apply_model_cox_BNT162b2_4_anytest
- apply_model_cox_ChAdOx_1_anytest
- apply_model_cox_ChAdOx_3_anytest
- apply_model_cox_ChAdOx_4_anytest
outputs:
moderately_sensitive:
plot: output/models_cox/images/hr_anytest_BNT162b2andChAdOx_*.png
## plot other outcomes BNT162b2andChAdOx
plot_hr_BNT162b2andChAdOx:
run: r:latest analysis/comparisons/plot_cox.R BNT162b2andChAdOx
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_BNT162b2_1_postest
- apply_model_cox_BNT162b2_1_covidadmitted
- apply_model_cox_BNT162b2_1_coviddeath
- apply_model_cox_BNT162b2_1_noncoviddeath
- apply_model_cox_BNT162b2_3_postest
- apply_model_cox_BNT162b2_3_covidadmitted
- apply_model_cox_BNT162b2_3_coviddeath
- apply_model_cox_BNT162b2_3_noncoviddeath
- apply_model_cox_BNT162b2_4_postest
- apply_model_cox_BNT162b2_4_covidadmitted
- apply_model_cox_BNT162b2_4_coviddeath
- apply_model_cox_BNT162b2_4_noncoviddeath
- apply_model_cox_ChAdOx_1_postest
- apply_model_cox_ChAdOx_1_covidadmitted
- apply_model_cox_ChAdOx_1_coviddeath
- apply_model_cox_ChAdOx_1_noncoviddeath
- apply_model_cox_ChAdOx_3_postest
- apply_model_cox_ChAdOx_3_covidadmitted
- apply_model_cox_ChAdOx_3_coviddeath
- apply_model_cox_ChAdOx_3_noncoviddeath
- apply_model_cox_ChAdOx_4_postest
- apply_model_cox_ChAdOx_4_covidadmitted
- apply_model_cox_ChAdOx_4_coviddeath
- apply_model_cox_ChAdOx_4_noncoviddeath
outputs:
moderately_sensitive:
plot: output/models_cox/images/hr_BNT162b2andChAdOx_*.png
## plot anytest BNT162b2vsChAdOx
plot_hr_anytest_BNT162b2vsChAdOx:
run: r:latest analysis/comparisons/plot_cox_anytest.R BNT162b2vsChAdOx
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_both_1_anytest
- apply_model_cox_both_3_anytest
- apply_model_cox_both_4_anytest
outputs:
moderately_sensitive:
plot: output/models_cox/images/hr_anytest_BNT162b2vsChAdOx_*.png
## plot other outcomes BNT162b2vsChAdOx
plot_hr_BNT162b2vsChAdOx:
run: r:latest analysis/comparisons/plot_cox.R BNT162b2vsChAdOx
needs:
- design
- data_2nd_vax_dates
- apply_model_cox_both_1_postest
- apply_model_cox_both_1_covidadmitted
- apply_model_cox_both_1_coviddeath
- apply_model_cox_both_1_noncoviddeath
- apply_model_cox_both_3_postest
- apply_model_cox_both_3_covidadmitted
- apply_model_cox_both_3_noncoviddeath
- apply_model_cox_both_4_postest
- apply_model_cox_both_4_covidadmitted
- apply_model_cox_both_4_coviddeath
- apply_model_cox_both_4_noncoviddeath
outputs:
moderately_sensitive:
plot: output/models_cox/images/hr_BNT162b2vsChAdOx_*.png
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 21:16:47
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- covid-ve-change-over-time-main
- Requested by
- Elsie Horne
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- bf4638e
- Requested actions
-
-
preflight_both_1_anytest
-
apply_model_cox_both_1_anytest
-
preflight_both_1_postest
-
apply_model_cox_both_1_postest
-
preflight_both_1_covidadmitted
-
apply_model_cox_both_1_covidadmitted
-
preflight_both_1_coviddeath
-
apply_model_cox_both_1_coviddeath
-
preflight_both_1_noncoviddeath
-
apply_model_cox_both_1_noncoviddeath
-
tables_model_cox_both_1
-
preflight_both_3_anytest
-
apply_model_cox_both_3_anytest
-
preflight_both_3_postest
-
apply_model_cox_both_3_postest
-
preflight_both_3_covidadmitted
-
apply_model_cox_both_3_covidadmitted
-
preflight_both_3_coviddeath
-
apply_model_cox_both_3_coviddeath
-
preflight_both_3_noncoviddeath
-
apply_model_cox_both_3_noncoviddeath
-
tables_model_cox_both_3
-
preflight_both_4_anytest
-
apply_model_cox_both_4_anytest
-
preflight_both_4_postest
-
apply_model_cox_both_4_postest
-
preflight_both_4_covidadmitted
-
apply_model_cox_both_4_covidadmitted
-
preflight_both_4_coviddeath
-
apply_model_cox_both_4_coviddeath
-
preflight_both_4_noncoviddeath
-
apply_model_cox_both_4_noncoviddeath
-
tables_model_cox_both_4
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plot_hr_anytest_BNT162b2
-
plot_hr_BNT162b2
-
plot_hr_anytest_ChAdOx
-
plot_hr_ChAdOx
-
plot_hr_anytest_BNT162b2andChAdOx
-
plot_hr_BNT162b2andChAdOx
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plot_hr_anytest_BNT162b2vsChAdOx
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plot_hr_BNT162b2vsChAdOx
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