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Job request: 5185

Organisation:
University of Bristol
Workspace:
covid-ve-change-over-time-main
ID:
whftuylb6lhbmmlh
View repo View project.yaml

This page shows the technical details of what happened when the 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 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:
    table1
    Status:
    Status: Succeeded
    Job identifier:
    t26j6ywarqioy742

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## #################################### 
  ## preliminaries 
  ## #################################### 

  design:
    run: r:latest analysis/design.R
    outputs:
      moderately_sensitive:
        study_dates_json: output/lib/study_parameters.json
        study_dates_rds: output/lib/study_parameters.rds
        jcvi_groups: output/lib/jcvi_groups.csv
        elig_dates: output/lib/elig_dates.csv
        regions: output/lib/regions.csv
        model_varlist: output/lib/model_varlist.rds
        outcomes: output/lib/outcomes.rds
        strata_vars: output/lib/strata_vars.rds
        subgroups: output/lib/subgroups.rds

  ## #################################### 
  ## study definition 
  ## #################################### 
  ## generate dummy data for study_definition 

  dummy_data:
    run: r:latest analysis/dummy_data.R
    needs:
    - design
    outputs:
      moderately_sensitive:
        dummy_data: analysis/dummy_data.feather

  ## study definition 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    dummy_data_file: analysis/dummy_data.feather
    needs:
    - design
    - dummy_data
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  ## #################################### 
  ## preprocessing 
  ## #################################### 
  ## process data from study_definition 

  data_input_process:
    run: r:latest analysis/preprocess/data_input_process.R
    needs:
    - design
    - dummy_data
    - generate_study_population
    outputs:
      highly_sensitive:
        data_wide_vax_dates: output/data/data_wide_vax_dates.rds
        data_long_shielded_dates: output/data/data_long_shielded_dates.rds
        data_long_nonshielded_dates: output/data/data_long_nonshielded_dates.rds
        data_long_bmi_dates: output/data/data_long_bmi_dates.rds
        data_processed: output/data/data_processed.rds
      moderately_sensitive:
        data_properties: output/tables/data_*_tabulate.txt

  ## apply eligiblity criteria from boxes a and b 

  data_eligible_ab:
    run: r:latest analysis/preprocess/data_eligible_ab.R
    needs:
    - design
    - data_input_process
    outputs:
      highly_sensitive:
        data_eligible_a: output/data/data_eligible_a.rds
        data_eligible_b: output/data/data_eligible_b.rds
      moderately_sensitive:
        eligibility_count: output/tables/eligibility_count_ab.txt
        group_age_ranges: output/lib/group_age_ranges.csv

  ## #################################### 
  ## second_vax_period 
  ## #################################### 
  ## identify second vaccination time periods 
  ## create dataset for identifying second vaccination time periods 

  data_2nd_vax_dates:
    run: r:latest analysis/second_vax_period/data_2nd_vax_dates.R
    needs:
    - design
    - data_input_process
    - data_eligible_ab
    outputs:
      highly_sensitive:
        data_vax_plot: output/second_vax_period/data/data_vax_plot.rds
        second_vax_period_dates_rds: output/second_vax_period/data/second_vax_period_dates.rds
      moderately_sensitive:
        second_vax_period_dates_txt: output/second_vax_period/tables/second_vax_period_dates.txt

  ## plot second vaccination time periods 

  plot_2nd_vax_dates:
    run: r:latest analysis/second_vax_period/plot_2nd_vax_dates.R
    needs:
    - design
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      moderately_sensitive:
        plots_by_region: output/second_vax_period/images/plot_by_region_*.png

  ## apply eligiblity criteria from boxes c, d and e 

  data_eligible_cde:
    run: r:latest analysis/second_vax_period/data_eligible_cde.R
    needs:
    - design
    - data_input_process
    - data_eligible_ab
    - data_2nd_vax_dates
    outputs:
      highly_sensitive:
        data_eligible_e_vax: output/data/data_eligible_e_vax.rds
        data_eligible_e_unvax: output/data/data_eligible_e_unvax.rds
        data_eligible_e: output/data/data_eligible_e.csv

  ## #################################### 
  ## study definition tests 
  ## #################################### 
  ## generate dummy data for study_definition_tests 

  dummy_data_tests:
    run: r:latest analysis/dummy_data_tests.R
    needs:
    - design
    - dummy_data
    - data_eligible_cde
    outputs:
      moderately_sensitive:
        dummy_data_tests: analysis/dummy_data_tests.feather

  ## study definition tests 

  generate_covid_tests_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_tests
      --output-format feather
    dummy_data_file: analysis/dummy_data_tests.feather
    needs:
    - design
    - data_eligible_cde
    - dummy_data_tests
    outputs:
      highly_sensitive:
        cohort: output/input_tests.feather

  ## check the tests data as expected and save processed data 

  process_tests:
    run: r:latest analysis/tests/process_tests.R
    needs:
    - design
    - data_input_process
    - data_eligible_cde
    - generate_covid_tests_data
    outputs:
      highly_sensitive:
        data_tests: output/data/data_tests.rds
        data_pregnancy: output/data/data_pregnancy.rds
      moderately_sensitive:
        covariate_distribution: output/tests/images/covariate_distribution.png

  ## #################################### 
  ## subsequent vaccination 
  ## #################################### 
  ## plot cumulative incidence of subsequent vaccination 

  plot_cumulative_incidence:
    run: r:latest analysis/subsequent_vax/plot_cumulative_incidence.R
    needs:
    - design
    - data_input_process
    - data_eligible_cde
    outputs:
      moderately_sensitive:
        ci_vax: output/subsequent_vax/images/ci_vax_*.png
        survtable: output/subsequent_vax/tables/survtable_*.txt

  ## #################################### 
  ## table 1 for report 
  ## #################################### 
  ## create table 1 for all and for each subgroup 

  table1:
    run: r:latest analysis/report/table1.R
    needs:
    - design
    - data_input_process
    - data_eligible_cde
    - process_tests
    outputs:
      moderately_sensitive:
        table_csv: output/report/tables/table1_*_REDACTED.csv
        table_html: output/report/tables/table1_*_REDACTED.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:20:48

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-ve-change-over-time-main
Requested by
Elsie Horne
Branch
main
Force run dependencies
No
Git commit hash
b3e1f6a
Requested actions
  • table1

Code comparison

Compare the code used in this Job Request