Job request: 6120

Organisation:: The UK Renal Registry
Workspace:: ckd-coverage-ve
ID:: drvx7nugesevrwju

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

Action:

cox_model_VE

Status:

Status: Succeeded

Job identifier:

oolhq35lgkt7en7h
Action:

cox_model_VE_matched

Status:

Status: Succeeded

Job identifier:

dtvcvh3v47dugohn
Action:

cox_VE_summary_matched

Status:

Status: Succeeded

Job identifier:

72cwemxdjl5xtfgk
Action:

cox_VE_summary

Status:

Status: Succeeded

Job identifier:

54unwgvrgl5qugfa

Pipeline

Show project.yaml

######################################
# Script defines project pipeline via series of actions
######################################

version: '3.0'

expectations:
  population_size: 300000

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
        
# Select cohort ----
  data_selection_coverage:
    run: r:latest analysis/coverage/data_selection_coverage.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_coverage.rds
        csv: output/data/data_cohort_coverage.csv
      moderately_sensitive:
        csv: output/tables/flowchart_coverage.csv

 # Data properties ----      
  data_properties:
    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*.txt
        
  # Table 1 ----
  table_1_coverage:
    run: r:latest analysis/coverage/table_1_coverage.R
    needs: [data_selection_coverage]
    outputs:
      highly_sensitive:
        data: output/tables/table1_coverage_redacted.rds
      moderately_sensitive:
        table: output/tables/table1_coverage_redacted.html
        
  # Cox models - dose-2 coverage ----
  cox_model:
    run: r:latest analysis/coverage/cox_model.R
    needs: [data_selection_coverage]
    outputs:
      highly_sensitive:
        data1: output/data/data_cox.rds
        data2: output/model/mod_strat_coxph_redacted.rds
        csv: output/data/data_cox.csv
      moderately_sensitive:
        csv: output/model/mod_strat_coxph_redacted.csv
        
  # Logistic models - dose-2 coverage ----
  logistic_model:
    run: r:latest analysis/coverage/logistic_model.R
    needs: [cox_model]
    outputs:
      highly_sensitive:
        data: 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, cox_model, logistic_model]
    outputs:
      moderately_sensitive:
        html: output/markdown/vaccine_coverage.html
        csv: output/tables/coverage_over_time_rounded.csv

  # 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

# Select cohort (VE) ----
  data_selection_VE:
    run: r:latest analysis/VE/data_selection_VE.R
    needs: [data_process]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_VE.rds
        csv: output/data/data_cohort_VE.csv
      moderately_sensitive:
        csv: output/tables/flowchart_VE.csv

  # Table 1 (VE) ----
  table_1_VE:
    run: r:latest analysis/VE/table_1_VE.R
    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
  table_irr:
    run: r:latest analysis/VE/table_irr.R
    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 ----
  cox_model_VE:
    run: r:latest analysis/VE/cox_model_VE.R
    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 ----
  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
        
# Select cohort (VE matched) ----
  data_selection_VE_matched:
    run: r:latest analysis/VE_matched/data_selection_VE_matched.R
    needs: [data_selection_VE]
    outputs:
      highly_sensitive:
        data: output/data/data_cohort_VE_matched.rds
        csv: output/data/data_cohort_VE_matched.csv
      moderately_sensitive:
        csv: output/tables/flowchart_VE_matched.csv

  # Table 1 (VE) ----
  table_1_VE_matched:
    run: r:latest analysis/VE_matched/table_1_VE.R
    needs: [data_selection_VE_matched]
    outputs:
      highly_sensitive:
        data: output/tables/table1_VE_matched_redacted.rds
      moderately_sensitive:
        table: output/tables/table1_VE_matched_redacted.html

  # Table IRR
  table_irr_matched:
    run: r:latest analysis/VE_matched/table_irr.R
    needs: [data_selection_VE_matched]
    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 ----
  cox_model_VE_matched:
    run: r:latest analysis/VE_matched/cox_model_VE.R
    needs: [data_selection_VE_matched, 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 ----
  cox_VE_summary_matched:
    run: r:latest -e 'rmarkdown::render("analysis/VE_matched/cox_VE_summary_matched.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output/markdown")'
    needs: [data_selection_VE_matched, 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: 2 years, 7 months ago 18 Mar 2022 19:59:23 UTC
Started: 2 years, 7 months ago 18 Mar 2022 20:00:24 UTC
Finished: 2 years, 7 months ago 18 Mar 2022 20:49:47 UTC
Runtime: 01:19:13

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: af510d5
Requested actions: cox_model_VE

cox_VE_summary

cox_model_VE_matched

cox_VE_summary_matched

Code comparison

Compare the code used in this Job Request