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project.yaml
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project.yaml
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######################################
# Script defines project pipeline via series of actions
######################################
version: '3.0'
expectations:
population_size: 250000
actions:
#############################
### Import/processing for coverage population
#############################
# Extract data ----
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition_coverage --output-dir=output/data
outputs:
highly_sensitive:
cohort: output/data/input.csv
# Process data ----
data_process:
run: r:latest analysis/data_process.R
needs: [generate_study_population]
outputs:
highly_sensitive:
data: output/data/data_processed.rds
csv: output/data/data_processed.csv
# Data properties (processed) ----
data_properties_process:
run: r:latest analysis/data_properties.R output/data/data_processed.rds output/data_properties
needs: [data_process]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed*.txt
#############################
### Import/processing for primary VE cohort
#############################
# Extract data - primary VE ----
generate_study_population_VE_primary:
run: cohortextractor:latest generate_cohort --study-definition study_definition_VE_primary --output-dir=output/data
outputs:
highly_sensitive:
cohort: output/data/input_VE_primary.csv
# Process data - primary VE ----
data_process_VE_primary:
run: r:latest analysis/data_process_VE_primary.R
needs: [generate_study_population_VE_primary]
outputs:
highly_sensitive:
data: output/data/data_processed_VE_primary.rds
csv: output/data/data_processed_VE_primary.csv
# Data properties (processed) - primary VE ----
data_properties_process_VE_primary:
run: r:latest analysis/data_properties.R output/data/data_processed_VE_primary.rds output/data_properties
needs: [data_process_VE_primary]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed_VE_primary*.txt
#############################
### Import/processing for booster VE cohort
#############################
# Extract data - booster VE ----
generate_study_population_VE_boost:
run: cohortextractor:latest generate_cohort --study-definition study_definition_VE_boost --output-dir=output/data
outputs:
highly_sensitive:
cohort: output/data/input_VE_boost.csv
# Process data - booster VE ----
data_process_VE_boost:
run: r:latest analysis/data_process_VE_boost.R
needs: [generate_study_population_VE_boost]
outputs:
highly_sensitive:
data: output/data/data_processed_VE_boost.rds
csv: output/data/data_processed_VE_boost.csv
# Data properties (processed) - booster VE ----
data_properties_process_VE_boost:
run: r:latest analysis/data_properties.R output/data/data_processed_VE_boost.rds output/data_properties
needs: [data_process_VE_boost]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_processed_VE_boost*.txt
#############################
### Coverage analyses
#############################
# Select cohort ----
data_selection_coverage:
run: r:latest analysis/coverage/data_selection_coverage.R
needs: [data_process]
outputs:
highly_sensitive:
data1: output/data/data_cohort_coverage.rds
csv: output/data/data_cohort_coverage.csv
data2: output/data/data_cohort_coverage_logistic.rds
data3: output/data/data_cohort_coverage_dose4.rds
moderately_sensitive:
csv: output/tables/flowchart_coverage.csv
# Data properties (coverage) ----
data_properties_coverage:
run: r:latest analysis/data_properties.R output/data/data_cohort_coverage.rds output/data_properties
needs: [data_selection_coverage]
outputs:
moderately_sensitive:
cohort: output/data_properties/data_cohort_coverage*.txt
# Table 1 primary outcome cohort (dose 3) ----
table_1_coverage_dose3:
run: r:latest analysis/coverage/table_1_coverage.R dose3
needs: [data_selection_coverage]
outputs:
highly_sensitive:
data: output/tables/table1_coverage_redacted_by_CKD.rds
moderately_sensitive:
table: output/tables/table1_coverage_redacted_by_CKD.html
# Table 1 primary outcome cohort (dose 3) ----
table_1_coverage_dose4:
run: r:latest analysis/coverage/table_1_coverage.R dose4
needs: [data_selection_coverage]
outputs:
highly_sensitive:
data: output/tables/table1_coverage_redacted_by_CKD_dose4.rds
moderately_sensitive:
table: output/tables/table1_coverage_redacted_by_CKD_dose4.html
# Cox models - dose-3 coverage ----
cox_model_dose3:
run: r:latest analysis/coverage/cox_model.R dose3
needs: [data_selection_coverage]
outputs:
highly_sensitive:
data1: output/data/data_cox_coverage_dose3*.rds
data2: output/model/mod_strat_coxph_redacted_dose3*.rds
moderately_sensitive:
csv: output/model/mod_strat_coxph_redacted_dose3*.csv
# Cox models - dose-4 coverage ----
cox_model_dose4:
run: r:latest analysis/coverage/cox_model.R dose4
needs: [data_selection_coverage]
outputs:
highly_sensitive:
data1: output/data/data_cox_coverage_dose4*.rds
data2: output/model/mod_strat_coxph_redacted_dose4*.rds
moderately_sensitive:
csv: output/model/mod_strat_coxph_redacted_dose4*.csv
# Logistic models - dose-3 coverage ----
logistic_model:
run: r:latest analysis/coverage/logistic_model.R
needs: [data_selection_coverage]
outputs:
highly_sensitive:
data1: output/data/data_lr.rds
data2: output/model/mod_strat_logistic_redacted.rds
moderately_sensitive:
csv: output/model/mod_strat_logistic_redacted.csv
# Coverage summaries ----
vaccine_coverage:
run: r:latest -e 'rmarkdown::render("analysis/coverage/vaccine_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
needs: [data_selection_coverage, table_1_coverage_dose3, table_1_coverage_dose4, cox_model_dose3, cox_model_dose4, logistic_model]
outputs:
moderately_sensitive:
html: output/markdown/vaccine_coverage.html
# Model checks ----
# Dose 3 - full
cox_model_check_coverage_dose3_full:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose3_full.html")' dose3 full
needs: [data_selection_coverage, cox_model_dose3]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose3_full.html
# Dose 3 - CKD3a
cox_model_check_coverage_dose3_CKD3a:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose3_CKD3a.html")' dose3 CKD3a
needs: [data_selection_coverage, cox_model_dose3]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose3_CKD3a.html
# Dose 3 - CKD3b
cox_model_check_coverage_dose3_CKD3b:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose3_CKD3b.html")' dose3 CKD3b
needs: [data_selection_coverage, cox_model_dose3]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose3_CKD3b.html
# Dose 3 - CKD4-5
cox_model_check_coverage_dose3_CKD4-5:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose3_CKD4-5.html")' dose3 CKD4-5
needs: [data_selection_coverage, cox_model_dose3]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose3_CKD4-5.html
# Dose 3 - dialysis
cox_model_check_coverage_dose3_dialysis:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose3_dialysis.html")' dose3 dialysis
needs: [data_selection_coverage, cox_model_dose3]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose3_dialysis.html
# Dose 3 - transplant
cox_model_check_coverage_dose3_transplant:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose3_transplant.html")' dose3 transplant
needs: [data_selection_coverage, cox_model_dose3]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose3_transplant.html
# Dose 4 - full
cox_model_check_coverage_dose4_full:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose4_full.html")' dose4 full
needs: [data_selection_coverage, cox_model_dose4]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose4_full.html
# Dose 4 - CKD3a
cox_model_check_coverage_dose4_CKD3a:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose4_CKD3a.html")' dose4 CKD3a
needs: [data_selection_coverage, cox_model_dose4]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose4_CKD3a.html
# Dose 4 - CKD3b
cox_model_check_coverage_dose4_CKD3b:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose4_CKD3b.html")' dose4 CKD3b
needs: [data_selection_coverage, cox_model_dose4]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose4_CKD3b.html
# Dose 4 - CKD4-5
cox_model_check_coverage_dose4_CKD4-5:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose4_CKD4-5.html")' dose4 CKD4-5
needs: [data_selection_coverage, cox_model_dose4]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose4_CKD4-5.html
# Dose 4 - dialysis
cox_model_check_coverage_dose4_dialysis:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose4_dialysis.html")' dose4 dialysis
needs: [data_selection_coverage, cox_model_dose4]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose4_dialysis.html
# Dose 4 - transplant
cox_model_check_coverage_dose4_transplant:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/coverage_model_checks/", output_file="dose4_transplant.html")' dose4 transplant
needs: [data_selection_coverage, cox_model_dose4]
outputs:
moderately_sensitive:
html: output/markdown/coverage_model_checks/dose4_transplant.html
#############################
### VE cohort selection - matched/unmatched
#############################
# Select cohort (single script used for both matched and unmatched analyses)
data_selection_VE_primary:
run: r:latest analysis/VE/data_selection_VE_primary.R
needs: [data_process_VE_primary]
outputs:
highly_sensitive:
data1: output/data/data_cohort_VE_primary.rds
data2: output/data/data_cohort_VE_primary_matched.rds
data3: output/lib/outcomes.rds
data4: output/lib/postvax_list.rds
csv1: output/data/data_cohort_VE_primary.csv
csv2: output/data/data_cohort_VE_primary_matched.csv
moderately_sensitive:
csv1: output/tables/flowchart_VE_primary.csv
csv2: output/tables/flowchart_VE_primary_matched.csv
# Descriptive plots of vaccination profile
vax_dates_VE:
run: r:latest -e 'rmarkdown::render("analysis/VE/vax_dates_VE.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown/")'
needs: [data_selection_coverage, data_selection_VE_primary]
outputs:
moderately_sensitive:
html: output/markdown/vax_dates_VE.html
#############################
### VE table 1 - all, CKD3, CKD4-5, RRT, Tx - matched,unmatched
#############################
# Table 1 (all unmatched)
table_1_VE_all_unmatched:
run: r:latest analysis/VE/table_1_VE.R unmatched all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table1_VE_primary_redacted_unmatched_all.rds
moderately_sensitive:
table: output/tables/table1_VE_primary_redacted_unmatched_all.html
# Table 1 (CKD3 unmatched)
table_1_VE_CKD3_unmatched:
run: r:latest analysis/VE/table_1_VE.R unmatched CKD3 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table1_VE_primary_redacted_unmatched_CKD3.rds
moderately_sensitive:
table: output/tables/table1_VE_primary_redacted_unmatched_CKD3.html
# Table 1 (CKD4-5 unmatched)
table_1_VE_CKD4_5_unmatched:
run: r:latest analysis/VE/table_1_VE.R unmatched CKD4-5 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table1_VE_primary_redacted_unmatched_CKD4-5.rds
moderately_sensitive:
table: output/tables/table1_VE_primary_redacted_unmatched_CKD4-5.html
# Table 1 (RRT unmatched)
table_1_VE_RRT_unmatched:
run: r:latest analysis/VE/table_1_VE.R unmatched RRT primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table1_VE_primary_redacted_unmatched_RRT.rds
moderately_sensitive:
table: output/tables/table1_VE_primary_redacted_unmatched_RRT.html
# Table 1 (Tx unmatched)
table_1_VE_Tx_unmatched:
run: r:latest analysis/VE/table_1_VE.R unmatched Tx primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table1_VE_primary_redacted_unmatched_Tx.rds
moderately_sensitive:
table: output/tables/table1_VE_primary_redacted_unmatched_Tx.html
# Table 1 (all matched)
table_1_VE_all_matched:
run: r:latest analysis/VE/table_1_VE.R matched all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table1_VE_primary_redacted_matched_all.rds
moderately_sensitive:
table: output/tables/table1_VE_primary_redacted_matched_all.html
#############################
### IRR - all, CKD3, CKD4-5, RRT - matched,unmatched
#############################
# Table IRR (all unmatched)
table_irr_unmatched_all:
run: r:latest analysis/VE/table_irr.R unmatched all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_unmatched_all.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_unmatched_all.csv
# Table IRR (CKD3 unmatched)
table_irr_unmatched_CKD3:
run: r:latest analysis/VE/table_irr.R unmatched CKD3 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_unmatched_CKD3.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_unmatched_CKD3.csv
# Table IRR (CKD4-5 unmatched)
table_irr_unmatched_CKD4_5:
run: r:latest analysis/VE/table_irr.R unmatched CKD4-5 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_unmatched_CKD4-5.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_unmatched_CKD4-5.csv
# Table IRR (RRT unmatched)
table_irr_unmatched_RRT:
run: r:latest analysis/VE/table_irr.R unmatched RRT primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_unmatched_RRT.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_unmatched_RRT.csv
# Table IRR (Tx unmatched)
table_irr_unmatched_Tx:
run: r:latest analysis/VE/table_irr.R unmatched Tx primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_unmatched_Tx.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_unmatched_Tx.csv
# Table IRR (all matched)
table_irr_matched_all:
run: r:latest analysis/VE/table_irr.R matched all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_matched_all.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_matched_all.csv
# Table IRR (CKD3 matched)
table_irr_matched_CKD3:
run: r:latest analysis/VE/table_irr.R matched CKD3 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_matched_CKD3.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_matched_CKD3.csv
# Table IRR (CKD4-5 matched)
table_irr_matched_CKD4_5:
run: r:latest analysis/VE/table_irr.R matched CKD4-5 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_matched_CKD4-5.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_matched_CKD4-5.csv
# Table IRR (RRT matched)
table_irr_matched_RRT:
run: r:latest analysis/VE/table_irr.R matched RRT primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_matched_RRT.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_matched_RRT.csv
# Table IRR (Tx matched)
table_irr_matched_Tx:
run: r:latest analysis/VE/table_irr.R matched Tx primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/tables/table_irr_primary_redacted_matched_Tx.rds
moderately_sensitive:
csv: output/tables/table_irr_primary_redacted_matched_Tx.csv
# Table IRR - verification (adapted from prior scripts)
table_irr_verification:
run: r:latest analysis/VE/table_irr_verification.R
needs: [data_selection_VE_primary]
outputs:
moderately_sensitive:
csv: output/tables/table_irr_redacted_verification_unmatched_all.csv
#############################
### Cox models - preflight then model
### Outcomes (4): postest, hosp, death, non-Covid death
### Populations (2): unmatched, matched
### Timescales (3): persontime, calendartime
### Subsets: all, CKD3, CKD4-5, RRT, Tx (unmatched)
#############################
### OUTCOME #1: covid_postest test
### unmatched persontime all
# preflight
cox_preflight_unmatched_persontime_covid_postest_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_postest all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_postest_all.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_postest_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_postest_all.txt
# model
cox_model_unmatched_persontime_covid_postest_VE_all:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_postest all primary
needs: [data_selection_VE_primary, table_irr_unmatched_all, cox_preflight_unmatched_persontime_covid_postest_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_all.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_postest_all.txt
### matched persontime all
# preflight
cox_preflight_matched_persontime_covid_postest_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R matched persontime covid_postest all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*matched_persontime_covid_postest_all.rds
formulas: output/model/VE_primary/formulas*matched_persontime_covid_postest_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_matched_persontime_covid_postest_all.txt
# model
cox_model_matched_persontime_covid_postest_VE_all:
run: r:latest analysis/VE/cox_model_VE.R matched persontime covid_postest all primary
needs: [data_selection_VE_primary, table_irr_matched_all, cox_preflight_matched_persontime_covid_postest_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*matched_persontime_covid_postest_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*matched_persontime_covid_postest_all.csv
logs: output/model/VE_primary/log_cox_model_matched_persontime_covid_postest_all.txt
### unmatched calendartime all
# preflight
cox_preflight_unmatched_calendartime_covid_postest_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched calendartime covid_postest all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_calendartime_covid_postest_all.rds
formulas: output/model/VE_primary/formulas*unmatched_calendartime_covid_postest_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_calendartime_covid_postest_all.txt
# model
cox_model_unmatched_calendartime_covid_postest_VE_all:
run: r:latest analysis/VE/cox_model_VE.R unmatched calendartime covid_postest all primary
needs: [data_selection_VE_primary, table_irr_unmatched_all, cox_preflight_unmatched_calendartime_covid_postest_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_calendartime_covid_postest_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_calendartime_covid_postest_all.csv
logs: output/model/VE_primary/log_cox_model_unmatched_calendartime_covid_postest_all.txt
### unmatched persontime CKD3
# preflight
cox_preflight_unmatched_persontime_covid_postest_VE_CKD3:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_postest CKD3 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_postest_CKD3.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_postest_CKD3.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_postest_CKD3.txt
# model
cox_model_unmatched_persontime_covid_postest_VE_CKD3:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_postest CKD3 primary
needs: [data_selection_VE_primary, table_irr_unmatched_CKD3, cox_preflight_unmatched_persontime_covid_postest_VE_CKD3]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_CKD3.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_CKD3.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_postest_CKD3.txt
### unmatched persontime CKD4-5
# preflight
cox_preflight_unmatched_persontime_covid_postest_VE_CKD4_5:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_postest CKD4-5 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_postest_CKD4-5.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_postest_CKD4-5.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_postest_CKD4-5.txt
# model
cox_model_unmatched_persontime_covid_postest_VE_CKD4_5:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_postest CKD4-5 primary
needs: [data_selection_VE_primary, table_irr_unmatched_CKD4_5, cox_preflight_unmatched_persontime_covid_postest_VE_CKD4_5]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_CKD4-5.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_CKD4-5.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_postest_CKD4-5.txt
### unmatched persontime RRT
# preflight
cox_preflight_unmatched_persontime_covid_postest_VE_RRT:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_postest RRT primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_postest_RRT.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_postest_RRT.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_postest_RRT.txt
# model
cox_model_unmatched_persontime_covid_postest_VE_RRT:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_postest RRT primary
needs: [data_selection_VE_primary, table_irr_unmatched_RRT, cox_preflight_unmatched_persontime_covid_postest_VE_RRT]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_RRT.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_RRT.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_postest_RRT.txt
### unmatched persontime Tx
# preflight
cox_preflight_unmatched_persontime_covid_postest_VE_Tx:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_postest Tx primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_postest_Tx.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_postest_Tx.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_postest_Tx.txt
# model
cox_model_unmatched_persontime_covid_postest_VE_Tx:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_postest Tx primary
needs: [data_selection_VE_primary, table_irr_unmatched_Tx, cox_preflight_unmatched_persontime_covid_postest_VE_Tx]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_Tx.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_postest_Tx.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_postest_Tx.txt
### OUTCOME #2: covid_hosp test
### unmatched persontime all
# preflight
cox_preflight_unmatched_persontime_covid_hosp_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_hosp all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_hosp_all.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_hosp_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_hosp_all.txt
# model
cox_model_unmatched_persontime_covid_hosp_VE_all:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_hosp all primary
needs: [data_selection_VE_primary, table_irr_unmatched_all, cox_preflight_unmatched_persontime_covid_hosp_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_all.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_hosp_all.txt
### matched persontime all
# preflight
cox_preflight_matched_persontime_covid_hosp_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R matched persontime covid_hosp all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*matched_persontime_covid_hosp_all.rds
formulas: output/model/VE_primary/formulas*matched_persontime_covid_hosp_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_matched_persontime_covid_hosp_all.txt
# model
cox_model_matched_persontime_covid_hosp_VE_all:
run: r:latest analysis/VE/cox_model_VE.R matched persontime covid_hosp all primary
needs: [data_selection_VE_primary, table_irr_matched_all, cox_preflight_matched_persontime_covid_hosp_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*matched_persontime_covid_hosp_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*matched_persontime_covid_hosp_all.csv
logs: output/model/VE_primary/log_cox_model_matched_persontime_covid_hosp_all.txt
### unmatched calendartime all
# preflight
cox_preflight_unmatched_calendartime_covid_hosp_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched calendartime covid_hosp all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_calendartime_covid_hosp_all.rds
formulas: output/model/VE_primary/formulas*unmatched_calendartime_covid_hosp_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_calendartime_covid_hosp_all.txt
# model
cox_model_unmatched_calendartime_covid_hosp_VE_all:
run: r:latest analysis/VE/cox_model_VE.R unmatched calendartime covid_hosp all primary
needs: [data_selection_VE_primary, table_irr_unmatched_all, cox_preflight_unmatched_calendartime_covid_hosp_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_calendartime_covid_hosp_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_calendartime_covid_hosp_all.csv
logs: output/model/VE_primary/log_cox_model_unmatched_calendartime_covid_hosp_all.txt
### unmatched persontime CKD3
# preflight
cox_preflight_unmatched_persontime_covid_hosp_VE_CKD3:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_hosp CKD3 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_hosp_CKD3.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_hosp_CKD3.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_hosp_CKD3.txt
# model
cox_model_unmatched_persontime_covid_hosp_VE_CKD3:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_hosp CKD3 primary
needs: [data_selection_VE_primary, table_irr_unmatched_CKD3, cox_preflight_unmatched_persontime_covid_hosp_VE_CKD3]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_CKD3.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_CKD3.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_hosp_CKD3.txt
### unmatched persontime CKD4-5
# preflight
cox_preflight_unmatched_persontime_covid_hosp_VE_CKD4_5:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_hosp CKD4-5 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_hosp_CKD4-5.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_hosp_CKD4-5.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_hosp_CKD4-5.txt
# model
cox_model_unmatched_persontime_covid_hosp_VE_CKD4_5:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_hosp CKD4-5 primary
needs: [data_selection_VE_primary, table_irr_unmatched_CKD4_5, cox_preflight_unmatched_persontime_covid_hosp_VE_CKD4_5]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_CKD4-5.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_CKD4-5.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_hosp_CKD4-5.txt
### unmatched persontime RRT
# preflight
cox_preflight_unmatched_persontime_covid_hosp_VE_RRT:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_hosp RRT primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_hosp_RRT.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_hosp_RRT.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_hosp_RRT.txt
# model
cox_model_unmatched_persontime_covid_hosp_VE_RRT:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_hosp RRT primary
needs: [data_selection_VE_primary, table_irr_unmatched_RRT, cox_preflight_unmatched_persontime_covid_hosp_VE_RRT]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_RRT.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_RRT.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_hosp_RRT.txt
### unmatched persontime Tx
# preflight
cox_preflight_unmatched_persontime_covid_hosp_VE_Tx:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_hosp Tx primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_hosp_Tx.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_hosp_Tx.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_hosp_Tx.txt
# model
cox_model_unmatched_persontime_covid_hosp_VE_Tx:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_hosp Tx primary
needs: [data_selection_VE_primary, table_irr_unmatched_Tx, cox_preflight_unmatched_persontime_covid_hosp_VE_Tx]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_Tx.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_hosp_Tx.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_hosp_Tx.txt
### OUTCOME #3: covid_death test
### unmatched persontime all
# preflight
cox_preflight_unmatched_persontime_covid_death_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_death all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_death_all.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_death_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_death_all.txt
# model
cox_model_unmatched_persontime_covid_death_VE_all:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_death all primary
needs: [data_selection_VE_primary, table_irr_unmatched_all, cox_preflight_unmatched_persontime_covid_death_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_all.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_death_all.txt
### matched persontime all
# preflight
cox_preflight_matched_persontime_covid_death_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R matched persontime covid_death all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*matched_persontime_covid_death_all.rds
formulas: output/model/VE_primary/formulas*matched_persontime_covid_death_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_matched_persontime_covid_death_all.txt
# model
cox_model_matched_persontime_covid_death_VE_all:
run: r:latest analysis/VE/cox_model_VE.R matched persontime covid_death all primary
needs: [data_selection_VE_primary, table_irr_matched_all, cox_preflight_matched_persontime_covid_death_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*matched_persontime_covid_death_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*matched_persontime_covid_death_all.csv
logs: output/model/VE_primary/log_cox_model_matched_persontime_covid_death_all.txt
### unmatched calendartime all
# preflight
cox_preflight_unmatched_calendartime_covid_death_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched calendartime covid_death all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_calendartime_covid_death_all.rds
formulas: output/model/VE_primary/formulas*unmatched_calendartime_covid_death_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_calendartime_covid_death_all.txt
# model
cox_model_unmatched_calendartime_covid_death_VE_all:
run: r:latest analysis/VE/cox_model_VE.R unmatched calendartime covid_death all primary
needs: [data_selection_VE_primary, table_irr_unmatched_all, cox_preflight_unmatched_calendartime_covid_death_VE_all]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_calendartime_covid_death_all.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_calendartime_covid_death_all.csv
logs: output/model/VE_primary/log_cox_model_unmatched_calendartime_covid_death_all.txt
### unmatched persontime CKD3
# preflight
cox_preflight_unmatched_persontime_covid_death_VE_CKD3:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_death CKD3 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_death_CKD3.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_death_CKD3.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_death_CKD3.txt
# model
cox_model_unmatched_persontime_covid_death_VE_CKD3:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_death CKD3 primary
needs: [data_selection_VE_primary, table_irr_unmatched_CKD3, cox_preflight_unmatched_persontime_covid_death_VE_CKD3]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_CKD3.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_CKD3.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_death_CKD3.txt
### unmatched persontime CKD4-5
# preflight
cox_preflight_unmatched_persontime_covid_death_VE_CKD4_5:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_death CKD4-5 primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_death_CKD4-5.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_death_CKD4-5.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_death_CKD4-5.txt
# model
cox_model_unmatched_persontime_covid_death_VE_CKD4_5:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_death CKD4-5 primary
needs: [data_selection_VE_primary, table_irr_unmatched_CKD4_5, cox_preflight_unmatched_persontime_covid_death_VE_CKD4_5]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_CKD4-5.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_CKD4-5.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_death_CKD4-5.txt
### unmatched persontime RRT
# preflight
cox_preflight_unmatched_persontime_covid_death_VE_RRT:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_death RRT primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_death_RRT.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_death_RRT.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_death_RRT.txt
# model
cox_model_unmatched_persontime_covid_death_VE_RRT:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_death RRT primary
needs: [data_selection_VE_primary, table_irr_unmatched_RRT, cox_preflight_unmatched_persontime_covid_death_VE_RRT]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_RRT.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_RRT.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_death_RRT.txt
### unmatched persontime Tx
# preflight
cox_preflight_unmatched_persontime_covid_death_VE_Tx:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime covid_death Tx primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_covid_death_Tx.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_covid_death_Tx.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_covid_death_Tx.txt
# model
cox_model_unmatched_persontime_covid_death_VE_Tx:
run: r:latest analysis/VE/cox_model_VE.R unmatched persontime covid_death Tx primary
needs: [data_selection_VE_primary, table_irr_unmatched_Tx, cox_preflight_unmatched_persontime_covid_death_VE_Tx]
outputs:
highly_sensitive:
data: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_Tx.rds
moderately_sensitive:
csv: output/model/VE_primary/modelcox*unmatched_persontime_covid_death_Tx.csv
logs: output/model/VE_primary/log_cox_model_unmatched_persontime_covid_death_Tx.txt
### OUTCOME #4: noncovid_death test
### unmatched persontime all
# preflight
cox_preflight_unmatched_persontime_noncovid_death_VE_all:
run: r:latest analysis/VE/cox_preflight_VE.R unmatched persontime noncovid_death all primary
needs: [data_selection_VE_primary]
outputs:
highly_sensitive:
data: output/model/VE_primary/data*unmatched_persontime_noncovid_death_all.rds
formulas: output/model/VE_primary/formulas*unmatched_persontime_noncovid_death_all.rds
moderately_sensitive:
logs: output/model/VE_primary/log_cox_preflight_unmatched_persontime_noncovid_death_all.txt
# model