Job request: 6453
- Organisation:
- University of Bristol
- Workspace:
- covid-ve-change-over-time--check-emergency-data
- ID:
- kzzezgfp2mepgppn
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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- Job identifier:
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paykwx4q2iuckwei
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omewakvz2k5rlmij
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3vqfufcgzdtdoroy
Pipeline
Show project.yaml
version: '3.0'
expectations:
population_size: 100000
actions:
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## DO NOT EDIT project.yaml or study_definition_1-6.py DIRECTLY
## These files are created by create-project.R
## Edit and run create-project.R to update the project.yaml
## Edit study_definition_k.py and run create-project.R to update
## study_definition_1-6.py
## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
## ####################################
## study definition
## ####################################
## generate dummy data for study_definition
dummy_data_vax:
run: r:latest analysis/dummy_data_vax.R
outputs:
moderately_sensitive:
dummy_data: analysis/dummy_data_vax.feather
## study definition
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
--output-format feather
dummy_data_file: analysis/dummy_data_vax.feather
needs:
- dummy_data_vax
outputs:
highly_sensitive:
cohort: output/input_vax.feather
## ####################################
## preprocessing
## ####################################
## process data from study_definition
data_input_process:
run: r:latest analysis/preprocess/data_input_process.R
needs:
- dummy_data_vax
- generate_study_population
outputs:
highly_sensitive:
data_wide_vax_dates: output/data/data_wide_vax_dates.rds
data_processed: output/data/data_processed.rds
moderately_sensitive:
data_properties: output/tables/data_*_tabulate.txt
## apply eligiblity criteria from boxes a and b
data_eligible_ab:
run: r:latest analysis/preprocess/data_eligible_ab.R
needs:
- data_input_process
outputs:
highly_sensitive:
data_eligible_a: output/data/data_eligible_a.rds
data_eligible_b: output/data/data_eligible_b.rds
moderately_sensitive:
eligibility_count_ab: output/tables/eligibility_count_ab.csv
group_age_ranges: output/lib/group_age_ranges.csv
## ####################################
## second_vax_period
## ####################################
## identify second vaccination time periods
## create dataset for identifying second vaccination time periods
data_2nd_vax_dates:
run: r:latest analysis/second_vax_period/data_2nd_vax_dates.R
needs:
- data_input_process
- data_eligible_ab
outputs:
highly_sensitive:
data_vax_plot: output/second_vax_period/data/data_vax_plot.rds
second_vax_period_dates_rds: output/second_vax_period/data/second_vax_period_dates.rds
moderately_sensitive:
second_vax_period_dates_txt: output/second_vax_period/tables/second_vax_period_dates.txt
## plot second vaccination time periods
plot_2nd_vax_dates:
run: r:latest analysis/second_vax_period/plot_2nd_vax_dates.R
needs:
- data_eligible_ab
- data_2nd_vax_dates
outputs:
moderately_sensitive:
plots_by_region: output/second_vax_period/images/plot_by_region_*.png
## apply eligiblity criteria from boxes c, d and e
data_eligible_cde:
run: r:latest analysis/preprocess/data_eligible_cde.R
needs:
- data_input_process
- data_eligible_ab
- data_2nd_vax_dates
outputs:
highly_sensitive:
data_eligible_e_vax: output/data/data_eligible_e_vax.rds
data_eligible_e_unvax: output/data/data_eligible_e_unvax.rds
data_eligible_e: output/data/data_eligible_e.csv
moderately_sensitive:
eligibility_count_cde: output/tables/eligibility_count_cde.csv
## ####################################
## study definition ever and k
## ####################################
## study definition ever
generate_ever_data:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ever
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_ever.feather
## study definition for period 1
generate_input_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition_1
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_1.feather
## study definition for period 2
generate_input_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition_2
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_2.feather
## study definition for period 3
generate_input_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition_3
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_3.feather
## study definition for period 4
generate_input_4:
run: cohortextractor:latest generate_cohort --study-definition study_definition_4
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_4.feather
## study definition for period 5
generate_input_5:
run: cohortextractor:latest generate_cohort --study-definition study_definition_5
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_5.feather
## study definition for period 6
generate_input_6:
run: cohortextractor:latest generate_cohort --study-definition study_definition_6
--output-format feather
needs:
- data_eligible_cde
outputs:
highly_sensitive:
cohort: output/input_6.feather
## ####################################
## process covariates data
## ####################################
## (includes anytest_date)
data_covariates_process:
run: r:latest analysis/preprocess/data_covariates_process.R
needs:
- data_input_process
- data_eligible_cde
- generate_ever_data
- generate_input_1
- generate_input_2
- generate_input_3
- generate_input_4
- generate_input_5
- generate_input_6
outputs:
highly_sensitive:
data_covariates: output/data/data_covariates.rds
## min and max follow-up dates for plots
data_min_max_fu:
run: r:latest analysis/comparisons/data_min_max_fu.R
needs:
- data_input_process
- data_covariates_process
outputs:
highly_sensitive:
data_min_max_fu: output/lib/data_min_max_fu.rds
## ####################################
## subsequent vaccination
## ####################################
## plot cumulative incidence of subsequent vaccination
plot_cumulative_incidence:
run: r:latest analysis/subsequent_vax/plot_cumulative_incidence.R
needs:
- data_input_process
- data_eligible_cde
outputs:
moderately_sensitive:
ci_vax: output/subsequent_vax/images/ci_vax.png
survtable: output/subsequent_vax/tables/survtable_redacted.csv
## ####################################
## table 1 for report
## ####################################
## create table 1 for all and for each subgroup
table1:
run: r:latest analysis/report/table1.R
needs:
- data_input_process
- data_eligible_cde
- data_covariates_process
outputs:
moderately_sensitive:
eligibility_count_p1: output/tables/eligibility_count_p1.csv
table_csv: output/report/tables/table1_*_REDACTED.csv
table_html: output/report/tables/table1_*_REDACTED.html
## ####################################
## process time to event data
## ####################################
## process tte data
data_tte_process_BNT162b2:
run: r:latest analysis/comparisons/data_tte_process.R BNT162b2
needs:
- data_input_process
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_BNT162b2*.rds
moderately_sensitive:
event_counts: output/tte/tables/event_counts_BNT162b2.csv
data_tte_process_ChAdOx1:
run: r:latest analysis/comparisons/data_tte_process.R ChAdOx1
needs:
- data_input_process
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_ChAdOx1*.rds
moderately_sensitive:
event_counts: output/tte/tables/event_counts_ChAdOx1.csv
data_tte_process_both:
run: r:latest analysis/comparisons/data_tte_process.R both
needs:
- data_input_process
- data_covariates_process
outputs:
highly_sensitive:
data_tte_brand_outcome: output/tte/data/data_tte_both*.rds
moderately_sensitive:
event_counts: output/tte/tables/event_counts_both.csv
## ####################################
## apply models
## ####################################
## BNT162b2; 65+ years; anytest
## preflight checks
preflight_BNT162b2_1_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_anytest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_1_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 anytest
needs:
- preflight_BNT162b2_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_anytest.txt
## BNT162b2; 65+ years; postest
## preflight checks
preflight_BNT162b2_1_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_postest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_1_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 postest
needs:
- preflight_BNT162b2_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_postest.txt
## BNT162b2; 65+ years; covidadmitted
## preflight checks
preflight_BNT162b2_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_1_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 covidadmitted
needs:
- preflight_BNT162b2_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_covidadmitted.txt
## BNT162b2; 65+ years; covidemergency
## preflight checks
preflight_BNT162b2_1_covidemergency:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_covidemergency*.txt
## apply cox model
apply_model_cox_BNT162b2_1_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 covidemergency
needs:
- preflight_BNT162b2_1_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_covidemergency.txt
## BNT162b2; 65+ years; coviddeath
## preflight checks
preflight_BNT162b2_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_1_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 coviddeath
needs:
- preflight_BNT162b2_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_coviddeath.txt
## BNT162b2; 65+ years; noncoviddeath
## preflight checks
preflight_BNT162b2_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 1 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_1_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_1_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_1_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_1_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 1 noncoviddeath
needs:
- preflight_BNT162b2_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_1_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_1_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_1_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_1_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_1_noncoviddeath.txt
## BNT162b2; 16-64 years and clinically vulnerable; anytest
## preflight checks
preflight_BNT162b2_2_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_anytest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_2_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 anytest
needs:
- preflight_BNT162b2_2_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_anytest.txt
## BNT162b2; 16-64 years and clinically vulnerable; postest
## preflight checks
preflight_BNT162b2_2_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_postest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_2_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 postest
needs:
- preflight_BNT162b2_2_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_postest.txt
## BNT162b2; 16-64 years and clinically vulnerable; covidadmitted
## preflight checks
preflight_BNT162b2_2_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_2_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 covidadmitted
needs:
- preflight_BNT162b2_2_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_covidadmitted.txt
## BNT162b2; 16-64 years and clinically vulnerable; covidemergency
## preflight checks
preflight_BNT162b2_2_covidemergency:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_covidemergency*.txt
## apply cox model
apply_model_cox_BNT162b2_2_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 covidemergency
needs:
- preflight_BNT162b2_2_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_covidemergency.txt
## BNT162b2; 16-64 years and clinically vulnerable; coviddeath
## preflight checks
preflight_BNT162b2_2_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_2_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 coviddeath
needs:
- preflight_BNT162b2_2_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_coviddeath.txt
## BNT162b2; 16-64 years and clinically vulnerable; noncoviddeath
## preflight checks
preflight_BNT162b2_2_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 2 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_2_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_2_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_2_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_2_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 2 noncoviddeath
needs:
- preflight_BNT162b2_2_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_2_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_2_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_2_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_2_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_2_noncoviddeath.txt
## BNT162b2; 40-64 years; anytest
## preflight checks
preflight_BNT162b2_3_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_anytest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_3_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 anytest
needs:
- preflight_BNT162b2_3_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_anytest.txt
## BNT162b2; 40-64 years; postest
## preflight checks
preflight_BNT162b2_3_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_postest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_3_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 postest
needs:
- preflight_BNT162b2_3_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_postest.txt
## BNT162b2; 40-64 years; covidadmitted
## preflight checks
preflight_BNT162b2_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_3_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 covidadmitted
needs:
- preflight_BNT162b2_3_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_covidadmitted.txt
## BNT162b2; 40-64 years; covidemergency
## preflight checks
preflight_BNT162b2_3_covidemergency:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_covidemergency*.txt
## apply cox model
apply_model_cox_BNT162b2_3_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 covidemergency
needs:
- preflight_BNT162b2_3_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_covidemergency.txt
## BNT162b2; 40-64 years; coviddeath
## preflight checks
preflight_BNT162b2_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_3_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 coviddeath
needs:
- preflight_BNT162b2_3_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_coviddeath.txt
## BNT162b2; 40-64 years; noncoviddeath
## preflight checks
preflight_BNT162b2_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 3 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_3_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_3_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_3_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_3_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 3 noncoviddeath
needs:
- preflight_BNT162b2_3_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_3_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_3_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_3_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_3_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_3_noncoviddeath.txt
## BNT162b2; 18-39 years; anytest
## preflight checks
preflight_BNT162b2_4_anytest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_anytest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_anytest*.txt
## apply cox model
apply_model_cox_BNT162b2_4_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 anytest
needs:
- preflight_BNT162b2_4_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_anytest.txt
## BNT162b2; 18-39 years; postest
## preflight checks
preflight_BNT162b2_4_postest:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_postest*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_postest*.txt
## apply cox model
apply_model_cox_BNT162b2_4_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 postest
needs:
- preflight_BNT162b2_4_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_postest.txt
## BNT162b2; 18-39 years; covidadmitted
## preflight checks
preflight_BNT162b2_4_covidadmitted:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_covidadmitted*.txt
## apply cox model
apply_model_cox_BNT162b2_4_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 covidadmitted
needs:
- preflight_BNT162b2_4_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_covidadmitted.txt
## BNT162b2; 18-39 years; covidemergency
## preflight checks
preflight_BNT162b2_4_covidemergency:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_covidemergency*.txt
## apply cox model
apply_model_cox_BNT162b2_4_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 covidemergency
needs:
- preflight_BNT162b2_4_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_covidemergency.txt
## BNT162b2; 18-39 years; coviddeath
## preflight checks
preflight_BNT162b2_4_coviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_coviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_4_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 coviddeath
needs:
- preflight_BNT162b2_4_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_coviddeath.txt
## BNT162b2; 18-39 years; noncoviddeath
## preflight checks
preflight_BNT162b2_4_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R BNT162b2 4 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_BNT162b2
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_BNT162b2_4_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_BNT162b2_4_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_BNT162b2_4_noncoviddeath*.txt
## apply cox model
apply_model_cox_BNT162b2_4_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R BNT162b2 4 noncoviddeath
needs:
- preflight_BNT162b2_4_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_BNT162b2_4_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_BNT162b2_4_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_BNT162b2_4_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_BNT162b2_4_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_BNT162b2_4_noncoviddeath.txt
## ChAdOx1; 65+ years; anytest
## preflight checks
preflight_ChAdOx1_1_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_1_anytest*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_anytest*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 anytest
needs:
- preflight_ChAdOx1_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_anytest.txt
## ChAdOx1; 65+ years; postest
## preflight checks
preflight_ChAdOx1_1_postest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_1_postest*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_postest*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 postest
needs:
- preflight_ChAdOx1_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_postest.txt
## ChAdOx1; 65+ years; covidadmitted
## preflight checks
preflight_ChAdOx1_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_1_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_covidadmitted*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 covidadmitted
needs:
- preflight_ChAdOx1_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_covidadmitted.txt
## ChAdOx1; 65+ years; covidemergency
## preflight checks
preflight_ChAdOx1_1_covidemergency:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_1_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_covidemergency*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 covidemergency
needs:
- preflight_ChAdOx1_1_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_covidemergency.txt
## ChAdOx1; 65+ years; coviddeath
## preflight checks
preflight_ChAdOx1_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_1_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_coviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 coviddeath
needs:
- preflight_ChAdOx1_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_coviddeath.txt
## ChAdOx1; 65+ years; noncoviddeath
## preflight checks
preflight_ChAdOx1_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 1 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_1_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_1_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_1_noncoviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_1_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 1 noncoviddeath
needs:
- preflight_ChAdOx1_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_1_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_1_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_1_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_1_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_1_noncoviddeath.txt
## ChAdOx1; 16-64 years and clinically vulnerable; anytest
## preflight checks
preflight_ChAdOx1_2_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_2_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_2_anytest*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_anytest*.txt
## apply cox model
apply_model_cox_ChAdOx1_2_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 anytest
needs:
- preflight_ChAdOx1_2_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_2_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_anytest.txt
## ChAdOx1; 16-64 years and clinically vulnerable; postest
## preflight checks
preflight_ChAdOx1_2_postest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_2_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_2_postest*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_postest*.txt
## apply cox model
apply_model_cox_ChAdOx1_2_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 postest
needs:
- preflight_ChAdOx1_2_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_2_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_postest.txt
## ChAdOx1; 16-64 years and clinically vulnerable; covidadmitted
## preflight checks
preflight_ChAdOx1_2_covidadmitted:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_2_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_2_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_covidadmitted*.txt
## apply cox model
apply_model_cox_ChAdOx1_2_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 covidadmitted
needs:
- preflight_ChAdOx1_2_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_2_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_covidadmitted.txt
## ChAdOx1; 16-64 years and clinically vulnerable; covidemergency
## preflight checks
preflight_ChAdOx1_2_covidemergency:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_2_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_2_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_covidemergency*.txt
## apply cox model
apply_model_cox_ChAdOx1_2_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 covidemergency
needs:
- preflight_ChAdOx1_2_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_2_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_covidemergency.txt
## ChAdOx1; 16-64 years and clinically vulnerable; coviddeath
## preflight checks
preflight_ChAdOx1_2_coviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_2_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_2_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_coviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_2_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 coviddeath
needs:
- preflight_ChAdOx1_2_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_2_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_coviddeath.txt
## ChAdOx1; 16-64 years and clinically vulnerable; noncoviddeath
## preflight checks
preflight_ChAdOx1_2_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 2 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_2_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_2_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_2_noncoviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_2_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 2 noncoviddeath
needs:
- preflight_ChAdOx1_2_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_2_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_2_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_2_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_2_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_2_noncoviddeath.txt
## ChAdOx1; 40-64 years; anytest
## preflight checks
preflight_ChAdOx1_3_anytest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_3_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_3_anytest*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_anytest*.txt
## apply cox model
apply_model_cox_ChAdOx1_3_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 anytest
needs:
- preflight_ChAdOx1_3_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_3_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_anytest.txt
## ChAdOx1; 40-64 years; postest
## preflight checks
preflight_ChAdOx1_3_postest:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_3_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_3_postest*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_postest*.txt
## apply cox model
apply_model_cox_ChAdOx1_3_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 postest
needs:
- preflight_ChAdOx1_3_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_3_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_postest.txt
## ChAdOx1; 40-64 years; covidadmitted
## preflight checks
preflight_ChAdOx1_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_3_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_3_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_covidadmitted*.txt
## apply cox model
apply_model_cox_ChAdOx1_3_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 covidadmitted
needs:
- preflight_ChAdOx1_3_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_3_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_covidadmitted.txt
## ChAdOx1; 40-64 years; covidemergency
## preflight checks
preflight_ChAdOx1_3_covidemergency:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_3_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_3_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_covidemergency*.txt
## apply cox model
apply_model_cox_ChAdOx1_3_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 covidemergency
needs:
- preflight_ChAdOx1_3_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_3_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_covidemergency.txt
## ChAdOx1; 40-64 years; coviddeath
## preflight checks
preflight_ChAdOx1_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_3_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_3_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_coviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_3_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 coviddeath
needs:
- preflight_ChAdOx1_3_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_3_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_coviddeath.txt
## ChAdOx1; 40-64 years; noncoviddeath
## preflight checks
preflight_ChAdOx1_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R ChAdOx1 3 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_ChAdOx1
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_ChAdOx1_3_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_ChAdOx1_3_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_ChAdOx1_3_noncoviddeath*.txt
## apply cox model
apply_model_cox_ChAdOx1_3_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R ChAdOx1 3 noncoviddeath
needs:
- preflight_ChAdOx1_3_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_ChAdOx1_3_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_ChAdOx1_3_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_ChAdOx1_3_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_ChAdOx1_3_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_ChAdOx1_3_noncoviddeath.txt
## both; 65+ years; anytest
## preflight checks
preflight_both_1_anytest:
run: r:latest analysis/comparisons/preflight.R both 1 anytest
needs:
- data_input_process
- data_covariates_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_update.R both 1 anytest
needs:
- preflight_both_1_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_1_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_anytest.txt
## both; 65+ years; postest
## preflight checks
preflight_both_1_postest:
run: r:latest analysis/comparisons/preflight.R both 1 postest
needs:
- data_input_process
- data_covariates_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_update.R both 1 postest
needs:
- preflight_both_1_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_1_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_postest.txt
## both; 65+ years; covidadmitted
## preflight checks
preflight_both_1_covidadmitted:
run: r:latest analysis/comparisons/preflight.R both 1 covidadmitted
needs:
- data_input_process
- data_covariates_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_update.R both 1 covidadmitted
needs:
- preflight_both_1_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_1_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_covidadmitted.txt
## both; 65+ years; covidemergency
## preflight checks
preflight_both_1_covidemergency:
run: r:latest analysis/comparisons/preflight.R both 1 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_1_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_1_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_both_1_covidemergency*.txt
## apply cox model
apply_model_cox_both_1_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 1 covidemergency
needs:
- preflight_both_1_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_1_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_covidemergency.txt
## both; 65+ years; coviddeath
## preflight checks
preflight_both_1_coviddeath:
run: r:latest analysis/comparisons/preflight.R both 1 coviddeath
needs:
- data_input_process
- data_covariates_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_update.R both 1 coviddeath
needs:
- preflight_both_1_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_1_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_coviddeath.txt
## both; 65+ years; noncoviddeath
## preflight checks
preflight_both_1_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R both 1 noncoviddeath
needs:
- data_input_process
- data_covariates_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_update.R both 1 noncoviddeath
needs:
- preflight_both_1_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_1_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_1_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_1_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_1_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_1_noncoviddeath.txt
## both; 16-64 years and clinically vulnerable; anytest
## preflight checks
preflight_both_2_anytest:
run: r:latest analysis/comparisons/preflight.R both 2 anytest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_2_anytest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_2_anytest*.html
preflight_report: output/preflight/tables/preflight_report_both_2_anytest*.txt
## apply cox model
apply_model_cox_both_2_anytest:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 anytest
needs:
- preflight_both_2_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_2_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_2_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_anytest.txt
## both; 16-64 years and clinically vulnerable; postest
## preflight checks
preflight_both_2_postest:
run: r:latest analysis/comparisons/preflight.R both 2 postest
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_2_postest*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_2_postest*.html
preflight_report: output/preflight/tables/preflight_report_both_2_postest*.txt
## apply cox model
apply_model_cox_both_2_postest:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 postest
needs:
- preflight_both_2_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_2_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_2_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_postest.txt
## both; 16-64 years and clinically vulnerable; covidadmitted
## preflight checks
preflight_both_2_covidadmitted:
run: r:latest analysis/comparisons/preflight.R both 2 covidadmitted
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_2_covidadmitted*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_2_covidadmitted*.html
preflight_report: output/preflight/tables/preflight_report_both_2_covidadmitted*.txt
## apply cox model
apply_model_cox_both_2_covidadmitted:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 covidadmitted
needs:
- preflight_both_2_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_2_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_2_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_covidadmitted.txt
## both; 16-64 years and clinically vulnerable; covidemergency
## preflight checks
preflight_both_2_covidemergency:
run: r:latest analysis/comparisons/preflight.R both 2 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_2_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_2_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_both_2_covidemergency*.txt
## apply cox model
apply_model_cox_both_2_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 covidemergency
needs:
- preflight_both_2_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_2_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_2_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_covidemergency.txt
## both; 16-64 years and clinically vulnerable; coviddeath
## preflight checks
preflight_both_2_coviddeath:
run: r:latest analysis/comparisons/preflight.R both 2 coviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_2_coviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_2_coviddeath*.html
preflight_report: output/preflight/tables/preflight_report_both_2_coviddeath*.txt
## apply cox model
apply_model_cox_both_2_coviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 coviddeath
needs:
- preflight_both_2_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_2_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_2_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_coviddeath.txt
## both; 16-64 years and clinically vulnerable; noncoviddeath
## preflight checks
preflight_both_2_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R both 2 noncoviddeath
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_2_noncoviddeath*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_2_noncoviddeath*.html
preflight_report: output/preflight/tables/preflight_report_both_2_noncoviddeath*.txt
## apply cox model
apply_model_cox_both_2_noncoviddeath:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 2 noncoviddeath
needs:
- preflight_both_2_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_2_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_2_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_2_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_2_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_2_noncoviddeath.txt
## both; 40-64 years; anytest
## preflight checks
preflight_both_3_anytest:
run: r:latest analysis/comparisons/preflight.R both 3 anytest
needs:
- data_input_process
- data_covariates_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_update.R both 3 anytest
needs:
- preflight_both_3_anytest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_anytest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_anytest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_3_anytest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_anytest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_anytest.txt
## both; 40-64 years; postest
## preflight checks
preflight_both_3_postest:
run: r:latest analysis/comparisons/preflight.R both 3 postest
needs:
- data_input_process
- data_covariates_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_update.R both 3 postest
needs:
- preflight_both_3_postest
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_postest*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_postest*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_3_postest*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_postest.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_postest.txt
## both; 40-64 years; covidadmitted
## preflight checks
preflight_both_3_covidadmitted:
run: r:latest analysis/comparisons/preflight.R both 3 covidadmitted
needs:
- data_input_process
- data_covariates_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_update.R both 3 covidadmitted
needs:
- preflight_both_3_covidadmitted
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_covidadmitted*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_covidadmitted*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_3_covidadmitted*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_covidadmitted.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_covidadmitted.txt
## both; 40-64 years; covidemergency
## preflight checks
preflight_both_3_covidemergency:
run: r:latest analysis/comparisons/preflight.R both 3 covidemergency
needs:
- data_input_process
- data_covariates_process
- data_tte_process_both
outputs:
highly_sensitive:
model_input: output/preflight/data/model_input_both_3_covidemergency*.rds
moderately_sensitive:
eventcheck_table: output/preflight/tables/eventcheck_both_3_covidemergency*.html
preflight_report: output/preflight/tables/preflight_report_both_3_covidemergency*.txt
## apply cox model
apply_model_cox_both_3_covidemergency:
run: r:latest analysis/comparisons/apply_model_cox_update.R both 3 covidemergency
needs:
- preflight_both_3_covidemergency
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_covidemergency*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_covidemergency*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_3_covidemergency*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_covidemergency.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_covidemergency.txt
## both; 40-64 years; coviddeath
## preflight checks
preflight_both_3_coviddeath:
run: r:latest analysis/comparisons/preflight.R both 3 coviddeath
needs:
- data_input_process
- data_covariates_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_update.R both 3 coviddeath
needs:
- preflight_both_3_coviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_coviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_coviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_3_coviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_coviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_coviddeath.txt
## both; 40-64 years; noncoviddeath
## preflight checks
preflight_both_3_noncoviddeath:
run: r:latest analysis/comparisons/preflight.R both 3 noncoviddeath
needs:
- data_input_process
- data_covariates_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_update.R both 3 noncoviddeath
needs:
- preflight_both_3_noncoviddeath
outputs:
highly_sensitive:
modelnumber: output/models_cox/data/model*_both_3_noncoviddeath*.rds
model_tidy_rds: output/models_cox/data/modelcox_tidy_both_3_noncoviddeath*.rds
model_glance_rds: output/models_cox/data/modelcox_glance_both_3_noncoviddeath*.rds
moderately_sensitive:
model_tidy_txt: output/models_cox/temp/modelcox_tidy_both_3_noncoviddeath.txt
model_glance_txt: output/models_cox/temp/modelcox_glance_both_3_noncoviddeath.txt
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 02:49:16
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Failed
- Backend
- TPP
- Requested by
- Elsie Horne
- Branch
- check-emergency-data
- Force run dependencies
- No
- Git commit hash
- 5cd972a
- Requested actions
-
-
preflight_BNT162b2_1_anytest
-
apply_model_cox_BNT162b2_1_anytest
-
preflight_BNT162b2_1_postest
-
apply_model_cox_BNT162b2_1_postest
-
preflight_BNT162b2_1_covidadmitted
-
apply_model_cox_BNT162b2_1_covidadmitted
-
preflight_BNT162b2_1_covidemergency
-
apply_model_cox_BNT162b2_1_covidemergency
-
preflight_BNT162b2_1_coviddeath
-
apply_model_cox_BNT162b2_1_coviddeath
-
preflight_BNT162b2_1_noncoviddeath
-
apply_model_cox_BNT162b2_1_noncoviddeath
-