Job request: 1056

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
pohjdp5pt3s5iywm succeeded 030_descriptive_mortality_rates.R
wnyu57jgq6jywglc succeeded 035_comparative_mortality_rates.R
x6jeigohycqxjujy succeeded 040_cause_of_death.R
kxscb7lalfo4rxyy succeeded 050_standardisation.R
zofsvnisgpuhfbdq succeeded 055_standardisation_smaller_age.R
lcvfdqq3azvi5yxt succeeded generate_sensitivity_measures_cohorts
2xqpn73eldyvlio5 succeeded generate_sensitivity_measures
oyl57min6snlsylt succeeded S020_sensitivity_baseline_characteristics_chdetail
wpbcwj4f2ytrjsiq succeeded S050_sensitivity_standardisation_chdetail
etjhsschqor4mkys succeeded S030_sensitivity_descriptive_mortality_rates_tpp

Pipeline

Show Hide project.yaml
version: "3.0"

expectations:
  population_size: 100000

actions:

# PRIMARY ANALYSES 
    
  generate_cohort_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-02-01" 
    outputs:
      highly_sensitive:
        cohort: output/input_2019-02-01.csv

  generate_cohort_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-02-01" 
    outputs:
      highly_sensitive:
        cohort: output/input_2020-02-01.csv

  generate_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2021-02-01 by month"
    outputs:
      highly_sensitive:
        cohort_measures: 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_age.csv
        measure2: output/measure_allcause_death_age.csv
        measure3: output/measure_noncovid_death_age.csv
        measure4: output/measure_covid_death_sex_age_five.csv
        measure5: output/measure_allcause_death_sex_age_five.csv
        measure6: output/measure_noncovid_death_sex_age_five.csv
        measure7: output/measure_covid_death_age_chdetail.csv
        measure8: output/measure_allcause_death_age_chdetail.csv
        measure9: output/measure_noncovid_death_age_chdetail.csv

  010_data_management_2019:
    run: r:latest analysis/010_data_management.R ./output/input_2019-02-01.csv ./output/study_population_2019.csv
    needs: [generate_cohort_2019]
    outputs: 
      highly_sensitive:
        data1: output/study_population_2019.csv

  010_data_management_2020:
    run: r:latest analysis/010_data_management.R ./output/input_2020-02-01.csv ./output/study_population_2020.csv
    needs: [generate_cohort_2020]
    outputs: 
      highly_sensitive:
        data2: output/study_population_2020.csv

  020_baseline_characteristics_2019:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2019.csv ./output/tables/table_1_2019.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        table1a: output/tables/table_1_2019.txt

  020_baseline_characteristics_2020:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2020.csv ./output/tables/table_one_2020.txt
    needs: [generate_cohort_2020, 010_data_management_2020]
    outputs: 
      moderately_sensitive:
        table1b: output/tables/table_one_2020.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_descriptive_allcause: output/tables/table_descriptive_allcause.txt
        table_descriptive_covid: output/tables/table_descriptive_covid.txt
        table_descriptive_noncovid: output/tables/table_descriptive_noncovid.txt
        plot_descriptive_allcause: output/plots/plot_descriptive_allcause.png
        plot_descriptive_covid: output/plots/plot_descriptive_covid.png
        plot_descriptive_noncovid: output/plots/plot_descriptive_noncovid.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_comparative_allcause: output/tables/table_comparative_allcause.txt
        table_comparative_covid: output/tables/table_comparative_covid.txt
        table_noncomparative_covid: output/tables/table_noncomparative_covid.txt
        plot_comparative_allcause: output/plots/plot_comparative_allcause.png
        plot_comparative_covid: output/plots/plot_comparative_covid.png
        plot_comparative_noncovid: output/plots/plot_comparative_noncovid.png

  040_cause_of_death.R:
    run: r:latest analysis/040_cause_of_death.R 
    needs: [generate_measures_cohorts]
    outputs: 
      moderately_sensitive:
        table_allcauses_ch: output/tables/table_allcauses_ch.txt
        table_allcauses_ph: output/tables/table_allcauses_ph.txt
        table_nccauses_ch: output/tables/table_nccauses_ch.txt
        table_nccauses_ph: output/tables/table_nccauses_ph.txt
        plot_allcauses_ch: output/plots/plot_allcauses_ch.png
        plot_allcauses_ph: output/plots/plot_allcauses_ph.png
        plot_nccauses_ch: output/plots/plot_nccauses_ch.png
        plot_nccauses_ph: output/plots/plot_nccauses_ph.png

  050_standardisation.R:
    run: r:latest analysis/050_standardisation.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_standardised_allcause: output/tables/table_standardised_allcause.txt
        table_standardised_covid: output/tables/table_standardised_covid.txt
        table_standardised_noncovid: output/tables/table_standardised_noncovid.txt     
        plot_standardised_allcause: output/plots/plot_standardised_allcause.png
        plot_standardised_covid: output/plots/plot_standardised_covid.png
        plot_standardised_noncovid: output/plots/plot_standardised_noncovid.png
        table_cmr_allcause: output/tables/table_cmr_allcause.txt
        table_cmr_covid: output/tables/table_cmr_covid.txt
        table_cmr_noncovid: output/tables/table_cmr_noncovid.txt
        plot_cmr_allcause: output/plots/plot_cmr_allcause.png
        plot_cmr_covid: output/plots/plot_cmr_covid.png
        plot_cmr_noncovid: output/plots/plot_cmr_noncovid.png


  055_standardisation_smaller_age.R:
    run: r:latest analysis/055_standardisation_smaller_age.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        table_standardised_allcause_age: output/tables/table_standardised_allcause_age.txt
        table_standardised_covid_age: output/tables/table_standardised_covid_age.txt
        table_standardised_noncovid_age: output/tables/table_standardised_noncovid_age.txt     
        plot_standardised_allcause_age_m: output/plots/plot_standardised_allcause_age_m.png
        plot_standardised_covid_age_m: output/plots/plot_standardised_covid_age_m.png
        plot_standardised_noncovid_age_m: output/plots/plot_standardised_noncovid_age_m.png
        plot_standardised_allcause_age_f: output/plots/plot_standardised_allcause_age_f.png
        plot_standardised_covid_age_f: output/plots/plot_standardised_covid_age_f.png
        plot_standardised_noncovid_age_f: output/plots/plot_standardised_noncovid_age_f.png
        table_cmr_allcause_age: output/tables/table_cmr_allcause_age.txt
        table_cmr_covid_age: output/tables/table_cmr_covid_age.txt
        table_cmr_noncovid_age: output/tables/table_cmr_noncovid_age.txt
        plot_cmr_allcause_age_m: output/plots/plot_cmr_allcause_age_m.png
        plot_cmr_covid_age_m: output/plots/plot_cmr_covid_age_m.png
        plot_cmr_noncovid_age_m: output/plots/plot_cmr_noncovid_age_m.png
        plot_cmr_allcause_age_f: output/plots/plot_cmr_allcause_age_f.png
        plot_cmr_covid_age_f: output/plots/plot_cmr_covid_age_f.png
        plot_cmr_noncovid_age_f: output/plots/plot_cmr_noncovid_age_f.png

# SENSITIVITY ANALYSES 

  generate_sensitivity_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sensitivity --index-date-range "2016-02-01 to 2021-02-01 by month"
    outputs:
      highly_sensitive:
        cohort_measures: output/input_sensitivity_*.csv

  generate_sensitivity_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_sensitivity
    needs: [generate_sensitivity_measures_cohorts]
    outputs:
      moderately_sensitive:
        measure1: output/measure_tpp_death_age.csv

  S020_sensitivity_baseline_characteristics_chdetail:
    run: r:latest analysis/S020_sensitivity_baseline_characteristics_chdetail.R ./output/study_population_2019.csv ./output/tables/S_table_one_chdetail_2019.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        S_table1: output/tables/S_table_one_chdetail_2019.txt

  S050_sensitivity_standardisation_chdetail:
    run: r:latest analysis/S050_sensitivity_standardisation_chdetail.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        S_table_standardised_allcause_chdetail: output/tables/S_table_standardised_allcause_chdetail.txt
        S_table_standardised_covid_chdetail: output/tables/S_table_standardised_covid_chdetail.txt
        S_table_standardised_noncovid_chdetail: output/tables/S_table_standardised_noncovid_chdetail.txt     
        S_plot_standardised_allcause_chdetail_m: output/plots/S_plot_standardised_allcause_chdetail_m.png
        S_plot_standardised_covid_chdetail_m: output/plots/S_plot_standardised_covid_chdetail_m.png
        S_plot_standardised_noncovid_chdetail_m: output/plots/S_plot_standardised_noncovid_chdetail_m.png
        S_plot_standardised_allcause_chdetail_f: output/plots/S_plot_standardised_allcause_chdetail_f.png
        S_plot_standardised_covid_chdetail_f: output/plots/S_plot_standardised_covid_chdetail_f.png
        S_plot_standardised_noncovid_chdetail_f: output/plots/S_plot_standardised_noncovid_chdetail_f.png

  S030_sensitivity_descriptive_mortality_rates_tpp:
    run: r:latest analysis/S030_sensitivity_descriptive_mortality_rates_tpp.R 
    needs: [generate_sensitivity_measures_cohorts, generate_sensitivity_measures]
    outputs: 
      moderately_sensitive:
        S_table_descriptive_allcause: output/tables/S_table_descriptive_allcause_tpp.txt
        S_plot_descriptive_noncovid: output/plots/S_plot_descriptive_allcause_tpp.png

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 02:58:43

Config

  • Backend:
    TPP
  • Workspace:
    carehome-noncarehome-death-research
  • Branch:
    master
  • Creator:
    annaschultze
  • Force run dependencies:
    False
  • Git Commit Hash:
    58c3efc
  • Requested actions:
    • 030_descriptive_mortality_rates.R
    • 035_comparative_mortality_rates.R
    • 040_cause_of_death.R
    • 050_standardisation.R
    • 055_standardisation_smaller_age.R
    • generate_sensitivity_measures_cohorts
    • generate_sensitivity_measures
    • S020_sensitivity_baseline_characteristics_chdetail
    • S050_sensitivity_standardisation_chdetail
    • S030_sensitivity_descriptive_mortality_rates_tpp