Job request: 611

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Anna Schultze requested one or more actions to be run against real patient data in the Carehome vs Non-Carehome Deaths 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

ID Status Action
pqwnr23nqa3zgkap succeeded generate_measures_cohorts
hl4cj2psk7svlkyt succeeded generate_measures
frcfxzygfim5pfyz succeeded 030_descriptive_mortality_rates.R
ymnlapca2cs6akl7 succeeded 035_comparative_mortality_rates.R
usjr6pnulpcatcy2 succeeded 040_cause_of_death.R
hbbdmh4auvgf6bld succeeded 050_standardisation.R
faiu6qfduumxsc6r succeeded generate_measures_sensitivity_cohort
ws6ru3jntlqvg37x succeeded generate_measures_sensitivity

Pipeline

Show Hide project.yaml
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_cohort_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019
    outputs:
      highly_sensitive:
        cohort: output/input_2019.csv

  generate_cohort_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2020
    outputs:
      highly_sensitive:
        cohort: output/input_2020.csv

  generate_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2020-11-30 by month"
    outputs:
      highly_sensitive:
        cohort1: output/input_measures_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures
    needs: [generate_measures_cohorts]
    outputs:
      moderately_sensitive:
        measure1: output/measure_covid_death_all.csv
        measure2: output/measure_covid_death_sex.csv
        measure3: output/measure_covid_death_age.csv
        measure4: output/measure_covid_death_sex_age.csv
        measure5: output/measure_allcause_death_all.csv
        measure6: output/measure_allcause_death_sex.csv
        measure7: output/measure_allcause_death_age.csv
        measure8: output/measure_allcause_death_sex_age.csv
        measure9: output/measure_noncovid_death_all.csv
        measure10: output/measure_noncovid_death_sex.csv
        measure11: output/measure_noncovid_death_age.csv
        measure12: output/measure_noncovid_death_sex_age.csv
        measure13: output/measure_covid_death_sex_age_five.csv
        measure14: output/measure_allcause_death_sex_age_five.csv
        measure15: output/measure_noncovid_death_sex_age_five.csv
        measure16: output/measure_covid_death_all_chdetail.csv
        measure17: output/measure_covid_death_sex_chdetail.csv
        measure18: output/measure_covid_death_age_chdetail.csv
        measure19: output/measure_covid_death_sex_age_chdetail.csv
        measure20: output/measure_allcause_death_all_chdetail.csv
        measure21: output/measure_allcause_death_sex_chdetail.csv
        measure22: output/measure_allcause_death_age_chdetail.csv
        measure23: output/measure_allcause_death_sex_age_chdetail.csv
        measure24: output/measure_noncovid_death_all_chdetail.csv
        measure25: output/measure_noncovid_death_sex_chdetail.csv
        measure26: output/measure_noncovid_death_age_chdetail.csv
        measure27: output/measure_noncovid_death_sex_age_chdetail.csv

  010_data_management_2019:
    run: r:latest analysis/010_data_management.R ./output/input_2019.csv ./data/study_population_2019.csv
    needs: [generate_cohort_2019]
    outputs: 
      highly_sensitive:
        data1: data/study_population_2019.csv

  010_data_management_2020:
    run: r:latest analysis/010_data_management.R ./output/input_2020.csv ./data/study_population_2020.csv
    needs: [generate_cohort_2020]
    outputs: 
      highly_sensitive:
        data2: data/study_population_2020.csv

  020_baseline_characteristics_2019:
    run: r:latest analysis/020_baseline_characteristics.R ./data/study_population_2019.csv ./analysis/outfiles/table_1a.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        table1a: analysis/outfiles/table_1a.txt

  020_baseline_characteristics_2020:
    run: r:latest analysis/020_baseline_characteristics.R ./data/study_population_2020.csv ./analysis/outfiles/table_1b.txt
    needs: [generate_cohort_2020, 010_data_management_2020]
    outputs: 
      moderately_sensitive:
        table1b: analysis/outfiles/table_1b.txt

  025_carehome_characteristics:
    run: r:latest analysis/025_carehome_characteristics.R ./data/study_population_2020.csv 
    needs: [010_data_management_2020]
    outputs: 
      moderately_sensitive:
        log: analysis/outfiles/carehome_characteristics.txt

  030_descriptive_mortality_rates.R:
    run: r:latest analysis/030_descriptive_mortality_rates.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_2a: analysis/outfiles/table_2a.txt
        table_2b: analysis/outfiles/table_2b.txt
        table_2c: analysis/outfiles/table_2c.txt
        table_2d: analysis/outfiles/table_2d.txt
        table_3a: analysis/outfiles/table_3a.txt
        table_3b: analysis/outfiles/table_3b.txt
        table_3c: analysis/outfiles/table_3c.txt
        table_3d: analysis/outfiles/table_3d.txt
        table_4a: analysis/outfiles/table_4a.txt
        table_4b: analysis/outfiles/table_4b.txt
        table_4c: analysis/outfiles/table_4c.txt
        table_4d: analysis/outfiles/table_4d.txt
        plot_1a: analysis/outfiles/plot_1a.png
        plot_1b: analysis/outfiles/plot_1b.png
        plot_1c: analysis/outfiles/plot_1c.png
        plot_2a: analysis/outfiles/plot_2a.png
        plot_2b: analysis/outfiles/plot_2b.png
        plot_2c: analysis/outfiles/plot_2c.png
        plot_3a: analysis/outfiles/plot_3a.png
        plot_3b: analysis/outfiles/plot_3b.png
        plot_3c: analysis/outfiles/plot_3c.png

  035_comparative_mortality_rates.R:
    run: r:latest analysis/035_comparative_mortality_rates.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_5a: analysis/outfiles/table_5a.txt
        table_5b: analysis/outfiles/table_5b.txt
        table_5c: analysis/outfiles/table_5c.txt
        table_5d: analysis/outfiles/table_5d.txt
        table_6a: analysis/outfiles/table_6a.txt
        table_6b: analysis/outfiles/table_6b.txt
        table_6c: analysis/outfiles/table_6c.txt
        table_6d: analysis/outfiles/table_6d.txt
        table_7a: analysis/outfiles/table_7a.txt
        table_7b: analysis/outfiles/table_7b.txt
        table_7c: analysis/outfiles/table_7c.txt
        table_7d: analysis/outfiles/table_7d.txt
        plot_8a: analysis/outfiles/plot_4a.png
        plot_8b: analysis/outfiles/plot_4b.png
        plot_8c: analysis/outfiles/plot_4c.png
        plot_5a: analysis/outfiles/plot_5a.png
        plot_5b: analysis/outfiles/plot_5b.png
        plot_5c: analysis/outfiles/plot_5c.png
        plot_6a: analysis/outfiles/plot_6a.png
        plot_6b: analysis/outfiles/plot_6b.png
        plot_6c: analysis/outfiles/plot_6c.png

  040_cause_of_death.R:
    run: r:latest analysis/040_cause_of_death.R 
    needs: [generate_measures_cohorts]
    outputs: 
      moderately_sensitive:
        table_8a: analysis/outfiles/table_8a.txt
        table_8b: analysis/outfiles/table_8b.txt
        plot_7a: analysis/outfiles/plot_7a.png
        plot_7b: analysis/outfiles/plot_7b.png

  050_standardisation.R:
    run: r:latest analysis/050_standardisation.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_9a: analysis/outfiles/table_9a.txt
        table_9b: analysis/outfiles/table_9b.txt     
        table_9c: analysis/outfiles/table_9c.txt
        plot_8a: analysis/outfiles/plot_8a.png
        plot_8b: analysis/outfiles/plot_8b.png
        plot_8c: analysis/outfiles/plot_8c.png

  generate_measures_sensitivity_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures_tppdeath --index-date-range "2019-02-01 to 2020-11-30 by month"
    needs: [generate_measures]
    outputs:
      highly_sensitive:
        cohort_sensitivity: output/input_measures_tppdeath_*.csv

  generate_measures_sensitivity:
    run: cohortextractor:latest generate_measures --study-definition study_definition_measures_tppdeath
    needs: [generate_measures_sensitivity_cohort]
    outputs:
      moderately_sensitive:
        measure_sensitivity: output/measure_allcause_tppdeath_all.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:03:41

Config

  • Backend:
    TPP
  • Workspace:
    carehome-noncarehome-death-research
  • Branch:
    master
  • Creator:
    annaschultze
  • Force run dependencies:
    True
  • Git Commit Hash:
    e400316
  • Requested actions:
    • generate_measures_cohorts
    • generate_measures
    • 030_descriptive_mortality_rates.R
    • 035_comparative_mortality_rates.R
    • 040_cause_of_death.R
    • 050_standardisation.R
    • generate_measures_sensitivity_cohort
    • generate_measures_sensitivity