Job request: 8898
- Organisation:
- The UK Renal Registry
- Workspace:
- ckd-coverage-ve
- ID:
- jjc7u5qxubpqikpf
This page shows the technical details of what happened when the authorised researcher Ed Parker requested one or more actions to be run against real patient data in the project, within a secure environment.
By cross-referencing the list of jobs with the
pipeline section below, you can infer what
security level
various outputs were written to. Researchers can never directly
view outputs marked as
highly_sensitive
;
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
-
- Job identifier:
-
o2rei65zlortzuab
Pipeline
Show project.yaml
######################################
# Script defines project pipeline via series of actions
######################################
version: '3.0'
expectations:
population_size: 100000
actions:
# Extract data ----
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --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
# 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
# Coverage summaries ----
cox_model_check_coverage:
run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check_coverage.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
needs: [data_selection_coverage, cox_model_dose3]
outputs:
moderately_sensitive:
html: output/markdown/cox_model_check_coverage.html
# Coverage summaries ----
# cox_model_check:
# run: r:latest -e 'rmarkdown::render("analysis/coverage/cox_model_check.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
# needs: [data_selection_coverage, cox_model]
# outputs:
# moderately_sensitive:
# html: output/markdown/cox_model_check.html
#############################
### VE - unmatched analyses
#############################
# Select cohort (single script used for both matched and unmatched analyses) ----
data_selection_VE:
run: r:latest analysis/VE/data_selection_VE.R
needs: [data_process]
outputs:
highly_sensitive:
data1: output/data/data_cohort_VE.rds
data2: output/data/data_cohort_VE_matched.rds
csv1: output/data/data_cohort_VE.csv
csv2: output/data/data_cohort_VE_matched.csv
moderately_sensitive:
csv1: output/tables/flowchart_VE.csv
csv2: output/tables/flowchart_VE_matched.csv
# Table 1 (VE unmatched) ----
table_1_VE:
run: r:latest analysis/VE/table_1_VE.R unmatched
needs: [data_selection_VE]
outputs:
highly_sensitive:
data: output/tables/table1_VE_redacted.rds
moderately_sensitive:
table: output/tables/table1_VE_redacted.html
# Table IRR (VE unmatched)
table_irr:
run: r:latest analysis/VE/table_irr.R unmatched
needs: [data_selection_VE]
outputs:
highly_sensitive:
data: output/tables/table_irr_redacted.rds
moderately_sensitive:
csv: output/tables/table_irr_redacted.csv
# Table IRR - verification (adapted from prior scripts)
table_irr_verification:
run: r:latest analysis/VE/table_irr_verification.R
needs: [data_selection_VE]
outputs:
moderately_sensitive:
csv: output/tables/table_irr_redacted_verification.csv
# Cox models - comparative VE unmatched ----
cox_model_VE:
run: r:latest analysis/VE/cox_model_VE.R unmatched
needs: [data_selection_VE, table_irr]
outputs:
highly_sensitive:
data: output/model/VE/modelcox*.rds
moderately_sensitive:
csv: output/model/VE/modelcox*.csv
txt: output/model/VE/modelcox*.txt
# Cox VE summaries for unmatched analysis ----
cox_VE_summary:
run: r:latest -e 'rmarkdown::render("analysis/VE/cox_VE_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
needs: [data_selection_VE, table_1_VE, table_irr, cox_model_VE]
outputs:
moderately_sensitive:
html: output/markdown/cox_VE_summary.html
# PLR models - comparative VE unmatched ----
plr_model_VE:
run: r:latest analysis/VE/plr_model_VE.R unmatched
needs: [data_selection_VE, table_irr]
outputs:
highly_sensitive:
data: output/model/VE_plr/modelplr*.rds
moderately_sensitive:
csv: output/model/VE_plr/modelplr*.csv
txt: output/model/VE_plr/modelplr*.txt
# PLR VE summaries for unmatched analysis ----
plr_VE_summary:
run: r:latest -e 'rmarkdown::render("analysis/VE/plr_VE_summary.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
needs: [data_selection_VE, table_1_VE, table_irr, plr_model_VE]
outputs:
moderately_sensitive:
html: output/markdown/plr_VE_summary.html
#############################
### VE - matched analyses
#############################
# Same scripts above but with matched argument in 'run'
# Table 1 (VE matched) ----
table_1_VE_matched:
run: r:latest analysis/VE/table_1_VE.R matched
needs: [data_selection_VE]
outputs:
highly_sensitive:
data: output/tables/table1_VE_matched_redacted.rds
moderately_sensitive:
table: output/tables/table1_VE_matched_redacted.html
# Table IRR (VE matched)
table_irr_matched:
run: r:latest analysis/VE/table_irr.R matched
needs: [data_selection_VE]
outputs:
highly_sensitive:
data: output/tables/table_irr_matched_redacted.rds
moderately_sensitive:
csv: output/tables/table_irr_matched_redacted.csv
# Cox models - comparative VE matched ----
cox_model_VE_matched:
run: r:latest analysis/VE/cox_model_VE.R matched
needs: [data_selection_VE, table_irr_matched]
outputs:
highly_sensitive:
data: output/model/VE_matched/modelcox*.rds
moderately_sensitive:
csv: output/model/VE_matched/modelcox*.csv
txt: output/model/VE_matched/modelcox*.txt
# Cox VE summaries for matched analysis ----
cox_VE_summary_matched:
run: r:latest -e 'rmarkdown::render("analysis/VE/cox_VE_summary_matched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
needs: [data_selection_VE, table_1_VE_matched, table_irr_matched, cox_model_VE_matched]
outputs:
moderately_sensitive:
html: output/markdown/cox_VE_summary_matched.html
# Check session info for set of packages ----
#session:
# run: r:latest -e 'rmarkdown::render("analysis/session.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
# needs: [data_selection]
# outputs:
# moderately_sensitive:
# html: output/markdown/session.html
Timeline
-
Created:
-
Started:
-
Finished:
-
Runtime: 00:02:17
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information
- Status
-
Succeeded
- Backend
- TPP
- Workspace
- ckd-coverage-ve
- Requested by
- Ed Parker
- Branch
- main
- Force run dependencies
- No
- Git commit hash
- 50bb869
- Requested actions
-
-
vaccine_coverage
-
Code comparison
Compare the code used in this Job Request