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Job request: 3548

Workspace:
carehome-noncarehome-death-research
ID:
yoimju36eo4fw734
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 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

Pipeline

Show 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_cohort_2wave:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-09-01" 
    outputs:
      highly_sensitive:
        cohort: output/input_2020-09-01.csv

  generate_cohort_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-02-01" 
    outputs:
      highly_sensitive:
        cohort: output/input_2021-02-01.csv

  generate_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_measures --index-date-range "2019-02-01 to 2021-03-31 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:
      highly_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
        measure14: output/measure_tested_covid.csv
        measure15: output/measure_admitted_covid.csv
        measure16: output/measure_admitted_any.csv
        measure17: output/measure_tested_covid_age.csv
        measure18: output/measure_admitted_covid_age.csv
        measure19: output/measure_admitted_any_age.csv
        measure20: output/measure_admitted_noncovid.csv
        measure21: output/measure_admitted_noncovid_age.csv
                
  010_data_management_2019:
    run: r:latest analysis/010_data_management.R ./output/input_2019-02-01.csv ./output/study_population_2019.csv ./output/study_population_new_2019.csv
    needs: [generate_cohort_2019]
    outputs: 
      highly_sensitive:
        data1: output/study_population_2019.csv
        data1_new: output/study_population_new_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 ./output/study_population_new_2020.csv
    needs: [generate_cohort_2020]
    outputs: 
      highly_sensitive:
        data2: output/study_population_2020.csv
        data2_new: output/study_population_new_2020.csv

  010_data_management_2wave:
    run: r:latest analysis/010_data_management.R ./output/input_2020-09-01.csv ./output/study_population_2wave.csv ./output/study_population_new_2wave.csv
    needs: [generate_cohort_2wave]
    outputs: 
      highly_sensitive:
        data3: output/study_population_2wave.csv
        data3_new: output/study_population_new_2wave.csv

  010_data_management_2021:
    run: r:latest analysis/010_data_management.R ./output/input_2021-02-01.csv ./output/study_population_2021.csv ./output/study_population_new_2021.csv
    needs: [generate_cohort_2021]
    outputs: 
      highly_sensitive:
        data4: output/study_population_2021.csv
        data4_new: output/study_population_new_2021.csv

  020_baseline_characteristics_2019:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2019.csv ./output/tables/1_table_descriptive_2019.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        table1a: output/tables/1_table_descriptive_2019.txt

  020_baseline_characteristics_2020:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2020.csv ./output/tables/1a_table_descriptive_2020.txt
    needs: [generate_cohort_2020, 010_data_management_2020]
    outputs: 
      moderately_sensitive:
        table1b: output/tables/1a_table_descriptive_2020.txt

  020_baseline_characteristics_2wave:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2wave.csv ./output/tables/1b_table_descriptive_2wave.txt
    needs: [generate_cohort_2wave, 010_data_management_2wave]
    outputs: 
      moderately_sensitive:
        table1c: output/tables/1b_table_descriptive_2wave.txt

  020_baseline_characteristics_2021:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_2021.csv ./output/tables/1c_table_descriptive_2021.txt
    needs: [generate_cohort_2021, 010_data_management_2021]
    outputs: 
      moderately_sensitive:
        table1d: output/tables/1c_table_descriptive_2021.txt

  020_baseline_characteristics_1wave_new:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_new_2020.csv ./output/tables/1d_table_descriptive_1wave_new.txt
    needs: [generate_cohort_2020, 010_data_management_2020]
    outputs: 
      moderately_sensitive:
        table1b: output/tables/1d_table_descriptive_1wave_new.txt

  020_baseline_characteristics_2wave_new:
    run: r:latest analysis/020_baseline_characteristics.R ./output/study_population_new_2wave.csv ./output/tables/1e_table_descriptive_2wave_new.txt
    needs: [generate_cohort_2wave, 010_data_management_2wave]
    outputs: 
      moderately_sensitive:
        table1b: output/tables/1e_table_descriptive_2wave_new.txt

  030_descriptive_mortality_rates:
    run: r:latest analysis/030_descriptive_mortality_rates.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        2_table_descriptive: output/tables/2*
        2_plot_descriptive: output/plots/2*

  035_comparative_mortality_rates:
    run: r:latest analysis/035_comparative_mortality_rates.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        3_table_comparative: output/tables/3*
        3_plot_comparative: output/plots/3*

  040_cause_of_death:
    run: r:latest analysis/040_cause_of_death.R 
    needs: [generate_measures_cohorts]
    outputs: 
      moderately_sensitive:
        4a_table_allcauses_ch: output/tables/4a_table_allcauses_ch.txt
        4c_table_nccauses_ch: output/tables/4c_table_nccauses_ch.txt
        4a_plot_allcauses_ch: output/plots/4a_plot_allcauses_ch.png
        4c_plot_nccauses_ch: output/plots/4c_plot_nccauses_ch.png

  050_standardisation:
    run: r:latest analysis/050_standardisation.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        5_table_standardised: output/tables/5*
        5_plot_standardised: output/plots/5*
        6_table_cmr: output/tables/6*
        6_plot_cmr: output/plots/6*

  055_standardisation_age_stratified:
    run: r:latest analysis/055_standardisation_age_stratified.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        7_table_standardised: output/tables/7*
        7_plot_standardised: output/plots/7*
        8_table_cmr: output/tables/8* 
        8_plot_cmr: output/plots/8*

# SENSITIVITY ANALYSES 

  generate_sensitivity_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sensitivity --index-date-range "2019-02-01 to 2021-03-31 by month"
    outputs:
      highly_sensitive:
        sens_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:
      highly_sensitive:
        SENS_measure4: output/measure_SENS_covid_death_sex_age_five.csv
        SENS_measure5: output/measure_SENS_allcause_death_sex_age_five.csv
        SENS_measure6: output/measure_SENS_noncovid_death_sex_age_five.csv

  S020_sensitivity_baseline_characteristics_chdetail:
    run: r:latest analysis/S020_sensitivity_baseline_characteristics_chdetail.R ./output/study_population_2019.csv ./output/tables/S1_table_descriptive_2019.txt
    needs: [generate_cohort_2019, 010_data_management_2019]
    outputs: 
      moderately_sensitive:
        S_table1: output/tables/S1_table_descriptive_2019.txt

  S050_sensitivity_standardisation_chdetail:
    run: r:latest analysis/S050_sensitivity_standardisation_chdetail.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        S2_table_standardised: output/tables/S2*
        S2_plot_standardised: output/plots/S2*

  S030_sensitivity_descriptive_test_admission:
    run: r:latest analysis/S030_sensitivity_descriptive_test_admission.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        S3_table_descriptive: output/tables/S3*
        S3_plot_descriptive: output/plots/S3*

  S050_sensitivity_standardisation_testing_admission:
    run: r:latest analysis/S050_sensitivity_standardisation_testing_admission.R 
    needs: [generate_measures_cohorts, generate_measures]
    outputs: 
      moderately_sensitive:
        S5_table_standardised: output/tables/S5*
        S5_plot_standardised: output/plots/S5*
        S6_table_cmr: output/tables/S6*
        S6_plot_cmr: output/plots/S6*

  S050_sensitivity_standardisation_expanded_chome:
    run: r:latest analysis/S050_sensitivity_standardisation_expanded_chome.R 
    needs: [generate_sensitivity_measures_cohorts, generate_sensitivity_measures]
    outputs: 
      moderately_sensitive:
        S7_table_standardised: output/tables/S7*
        S7_plot_standardised: output/plots/S7*
        S8_table_cmr: output/tables/S8*
        S8_plot_cmr: output/plots/S8*

  generate_comorb_measures_cohorts:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_comorbidities --index-date-range "2019-02-01 to 2021-03-31 by month"
    outputs:
      highly_sensitive:
        comorb_cohort_measures: output/input_comorbidities*

  generate_comorb_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_comorbidities
    needs: [generate_comorb_measures_cohorts]
    outputs:
      moderately_sensitive:
        dementia: output/measure_COMORB_dementia.csv 
        stroke: output/measure_COMORB_stroke.csv 
        cancer: output/measure_COMORB_cancer.csv 
        chronic_cardiac_disease: output/measure_COMORB_chronic_cardiac_disease.csv 
        chronic_respiratory_disease: output/measure_COMORB_chronic_respiratory_disease.csv 
        chronic_liver_disease: output/measure_COMORB_chronic_liver_disease.csv 
        diabetes: output/measure_COMORB_diabetes.csv 

  S_comorbidity_plots:
    run: r:latest analysis/S_comorbidity_plots.R 
    needs: [generate_comorb_measures]
    outputs: 
      moderately_sensitive:
        S9_plots*: output/plots/S9*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 19:04:36

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

Job information

Status
Succeeded
Backend
TPP
Workspace
carehome-noncarehome-death-research
Requested by
Anna Schultze
Branch
master
Force run dependencies
Yes
Git commit hash
64e31e3
Requested actions
  • run_all