Skip to content

Job request: 3969

Workspace:
post-admissions-admissions-kb
ID:
cskfghlgjxqfubfm

This page shows the technical details of what happened when authorised researcher Krishnan Bhaskaran 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: 1000

actions:

  generate_suseth:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_suseth
    outputs:
      highly_sensitive:
        cohort: output/input_suseth.csv

  generate_study_pop_covdischarged:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covdischarged
    outputs:
      highly_sensitive:
        cohort: output/input_covdischarged.csv

  generate_study_pop_pneum2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_pneum2019
    outputs:
      highly_sensitive:
        cohort: output/input_pneum2019.csv

  generate_study_pop_flu2017_19:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_flu2017_19
    outputs:
      highly_sensitive:
        cohort: output/input_flu2017_19.csv

        
  generate_2019pool02:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool02
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool02.csv        

  generate_2019pool02_ALT:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019 --index-date-range "2019-02-01"
    outputs:
      highly_sensitive:
        cohort: output/input_2019_2019-02-01.csv        

  generate_2019pool03:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool03
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool03.csv        

  generate_2019pool04:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool04
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool04.csv        

  generate_2019pool05:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool05
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool05.csv        

  generate_2019pool06:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool06
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool06.csv        

  generate_2019pool07:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool07
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool07.csv        

  generate_2019pool08:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool08
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool08.csv        
           
  generate_2019pool09:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool09
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool09.csv        

  generate_2019pool10:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool10
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool10.csv        
      
  generate_2019pool11:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool11
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool11.csv        

  generate_2019pool12:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2019pool12
    outputs:
      highly_sensitive:
        cohort: output/input_2019pool12.csv        
                   
  create_covid:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do COVID
    needs: [generate_study_pop_covdischarged]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_COVID.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_COVID.log

  create_pneum2019:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do PNEUM 
    needs: [generate_study_pop_pneum2019]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_PNEUM.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_PNEUM.log
 
  create_flu2017_19:
    run: stata-mp:latest analysis/cr_create_analysis_dataset.do FLU 
    needs: [generate_study_pop_flu2017_19]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_analysis_dataset_FLU.dta
      moderately_sensitive:
        log: analysis/output/cr_create_analysis_dataset_FLU.log

  create_2019pool02:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 02
    needs: [generate_2019pool02]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_02.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_02.log

  create_2019pool03:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 03
    needs: [generate_2019pool03]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_03.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_03.log

  create_2019pool04:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 04
    needs: [generate_2019pool04]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_04.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_04.log

  create_2019pool05:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 05
    needs: [generate_2019pool05]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_05.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_05.log

  create_2019pool06:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 06
    needs: [generate_2019pool06]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_06.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_06.log

  create_2019pool07:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 07
    needs: [generate_2019pool07]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_07.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_07.log

  create_2019pool08:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 08
    needs: [generate_2019pool08]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_08.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_08.log

  create_2019pool09:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 09
    needs: [generate_2019pool09]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_09.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_09.log

  create_2019pool10:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 10
    needs: [generate_2019pool10]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_10.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_10.log

  create_2019pool11:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 11
    needs: [generate_2019pool11]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_11.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_11.log

  create_2019pool12:
    run: stata-mp:latest analysis/cr_create_2019pool_data.do 12
    needs: [generate_2019pool12]
    outputs:
      highly_sensitive:
        cohort: analysis/cr_create_2019pool_data_12.dta
      moderately_sensitive:
        log: analysis/output/cr_create_2019pool_data_12.log


  getmatches2019:
    run: stata-mp:latest analysis/cr_getmatches2019.do
    needs:
      - create_covid
      - create_2019pool02
      - create_2019pool03
      - create_2019pool04
      - create_2019pool05
      - create_2019pool06
      - create_2019pool07
      - create_2019pool08
      - create_2019pool09
      - create_2019pool10
      - create_2019pool11
      - create_2019pool12
    outputs:
      highly_sensitive:
        cohort: analysis/cr_getmatches2019.dta
      moderately_sensitive:
        log: analysis/output/cr_getmatches2019.log

  appenddata:
    run: stata-mp:latest analysis/cr_append_process_data.do
    needs:
      - create_covid
      - create_pneum2019
      - create_flu2017_19
      - generate_suseth
      - getmatches2019
    outputs:
      highly_sensitive:
        cohort: analysis/cr_append_process_data.dta
      moderately_sensitive:
        log: analysis/output/cr_append_process_data.log

  andescriptives_models:
    run: stata-mp:latest analysis/model_descriptives_models.do
    needs: 
      - generate_study_pop_covdischarged
      - appenddata
    outputs:
      moderately_sensitive:
        logs: analysis/output/*.log 
        tables: analysis/output/an_*.txt
        figures: analysis/output/an_cumulativeincidence*.svg
        timefig: analysis/output/an_desc*.svg
        models: analysis/output/models/an_cox*.ster

  ancoxMI:
    run: stata-mp:latest analysis/an_cox_R2.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_R2.log
        models: analysis/output/models/an_cox_R2*.ster
         
  anFGcirculatory:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do circulatory 23498
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2circulatory.log
        models: analysis/output/models/an_FG_causespecific_R2circulatory*.ster
 
  anFGcancer_ex_nmsc:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do cancer_ex_nmsc 54668
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_FG_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anFGrespiratory:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do respiratory 1309
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2respiratory.log
        models: analysis/output/models/an_FG_causespecific_R2respiratory*.ster
 
 
  anFGrespiratorylrti:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do respiratorylrti 235
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_FG_causespecific_R2respiratorylrti*.ster
  
  
  anFGdigestive:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do digestive 32463
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2digestive.log
        models: analysis/output/models/an_FG_causespecific_R2digestive*.ster
  
  
  anFGmentalhealth:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do mentalhealth 25465
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_FG_causespecific_R2mentalhealth*.ster
  
 
  anFGnervoussystem:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do nervoussystem 2355
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_FG_causespecific_R2nervoussystem*.ster
  
  
  anFGgenitourinary:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do genitourinary 239802
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2genitourinary.log
        models: analysis/output/models/an_FG_causespecific_R2genitourinary*.ster
  
  
  anFGendo_nutr_metabol:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do endo_nutr_metabol 155545
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_FG_causespecific_R2endo_nutr_metabol*.ster
  
  
  anFGexternal:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do external 125554
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2external.log
        models: analysis/output/models/an_FG_causespecific_R2external*.ster
  
  
  anFGmusculoskeletal:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do musculoskeletal 124
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_FG_causespecific_R2musculoskeletal*.ster
  
  
  anFGotherinfections:
    run: stata-mp:latest analysis/an_FG_causespecific_R2.do otherinfections 789
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FG_causespecific_R2otherinfections.log
        models: analysis/output/models/an_FG_causespecific_R2otherinfections*.ster

  anCOXr2circulatory:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do circulatory 23498
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2circulatory.log
        models: analysis/output/models/an_cox_causespecific_R2circulatory*.ster
 
  anCOXr2cancer_ex_nmsc:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do cancer_ex_nmsc 54668
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_cox_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anCOXr2respiratory:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do respiratory 1309
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2respiratory.log
        models: analysis/output/models/an_cox_causespecific_R2respiratory*.ster
 
 
  anCOXr2respiratorylrti:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do respiratorylrti 235
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_cox_causespecific_R2respiratorylrti*.ster
  
  
  anCOXr2digestive:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do digestive 32463
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2digestive.log
        models: analysis/output/models/an_cox_causespecific_R2digestive*.ster
  
  
  anCOXr2mentalhealth:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do mentalhealth 25465
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_cox_causespecific_R2mentalhealth*.ster
  
 
  anCOXr2nervoussystem:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do nervoussystem 2355
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_cox_causespecific_R2nervoussystem*.ster
  
  
  anCOXr2genitourinary:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do genitourinary 239802
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2genitourinary.log
        models: analysis/output/models/an_cox_causespecific_R2genitourinary*.ster
  
  
  anCOXr2endo_nutr_metabol:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do endo_nutr_metabol 155545
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_cox_causespecific_R2endo_nutr_metabol*.ster
  
  
  anCOXr2external:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do external 125554
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2external.log
        models: analysis/output/models/an_cox_causespecific_R2external*.ster
  
  
  anCOXr2musculoskeletal:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do musculoskeletal 124
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_cox_causespecific_R2musculoskeletal*.ster
  
  
  anCOXr2otherinfections:
    run: stata-mp:latest analysis/an_cox_causespecific_R2.do otherinfections 789
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_cox_causespecific_R2otherinfections.log
        models: analysis/output/models/an_cox_causespecific_R2otherinfections*.ster


  ancoxbytime:
    run: stata-mp:latest analysis/an_coxbytime_R2.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_R2.log
        models: analysis/output/models/an_coxbytime_R2*.ster

  anFGbytimecirculatory:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do circulatory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2circulatory.log
        models: analysis/output/models/an_FGbytime_causespecific_R2circulatory*.ster
 
  anFGbytimecancer_ex_nmsc:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do cancer_ex_nmsc 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_FGbytime_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anFGbytimerespiratory:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do respiratory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2respiratory.log
        models: analysis/output/models/an_FGbytime_causespecific_R2respiratory*.ster
 
 
  anFGbytimerespiratorylrti:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do respiratorylrti 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_FGbytime_causespecific_R2respiratorylrti*.ster
  
  
  anFGbytimedigestive:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do digestive 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2digestive.log
        models: analysis/output/models/an_FGbytime_causespecific_R2digestive*.ster
  
  
  anFGbytimementalhealth:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do mentalhealth 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_FGbytime_causespecific_R2mentalhealth*.ster
  
 
  anFGbytimenervoussystem:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do nervoussystem 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_FGbytime_causespecific_R2nervoussystem*.ster
  
  
  anFGbytimegenitourinary:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do genitourinary 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2genitourinary.log
        models: analysis/output/models/an_FGbytime_causespecific_R2genitourinary*.ster
  
  
  anFGbytimeendo_nutr_metabol:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do endo_nutr_metabol 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_FGbytime_causespecific_R2endo_nutr_metabol*.ster
  
  
  anFGbytimeexternal:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do external 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2external.log
        models: analysis/output/models/an_FGbytime_causespecific_R2external*.ster
  
  
  anFGbytimemusculoskeletal:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do musculoskeletal 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_FGbytime_causespecific_R2musculoskeletal*.ster
  
  
  anFGbytimeotherinfections:
    run: stata-mp:latest analysis/an_FGbytime_causespecific_R2.do otherinfections 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_FGbytime_causespecific_R2otherinfections.log
        models: analysis/output/models/an_FGbytime_causespecific_R2otherinfections*.ster


  anCOXr2bytimecirculatory:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do circulatory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2circulatory.log
        models: analysis/output/models/an_coxbytime_causespecific_R2circulatory*.ster
 
  anCOXr2bytimecancer_ex_nmsc:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do cancer_ex_nmsc 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2cancer_ex_nmsc.log
        models: analysis/output/models/an_coxbytime_causespecific_R2cancer_ex_nmsc*.ster
 
  
  anCOXr2bytimerespiratory:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do respiratory 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2respiratory.log
        models: analysis/output/models/an_coxbytime_causespecific_R2respiratory*.ster
 
 
  anCOXr2bytimerespiratorylrti:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do respiratorylrti 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2respiratorylrti.log
        models: analysis/output/models/an_coxbytime_causespecific_R2respiratorylrti*.ster
  
  
  anCOXr2bytimedigestive:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do digestive 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2digestive.log
        models: analysis/output/models/an_coxbytime_causespecific_R2digestive*.ster
  
  
  anCOXr2bytimementalhealth:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do mentalhealth 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2mentalhealth.log
        models: analysis/output/models/an_coxbytime_causespecific_R2mentalhealth*.ster
  
 
  anCOXr2bytimenervoussystem:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do nervoussystem 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2nervoussystem.log
        models: analysis/output/models/an_coxbytime_causespecific_R2nervoussystem*.ster
  
  
  anCOXr2bytimegenitourinary:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do genitourinary 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2genitourinary.log
        models: analysis/output/models/an_coxbytime_causespecific_R2genitourinary*.ster
  
  
  anCOXr2bytimeendo_nutr_metabol:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do endo_nutr_metabol 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2endo_nutr_metabol.log
        models: analysis/output/models/an_coxbytime_causespecific_R2endo_nutr_metabol*.ster
  
  
  anCOXr2bytimeexternal:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do external 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2external.log
        models: analysis/output/models/an_coxbytime_causespecific_R2external*.ster
  
  
  anCOXr2bytimemusculoskeletal:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do musculoskeletal 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2musculoskeletal.log
        models: analysis/output/models/an_coxbytime_causespecific_R2musculoskeletal*.ster
  
  
  anCOXr2bytimeotherinfections:
    run: stata-mp:latest analysis/an_coxbytime_causespecific_R2.do otherinfections 
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_coxbytime_causespecific_R2otherinfections.log
        models: analysis/output/models/an_coxbytime_causespecific_R2otherinfections*.ster
  
 
  anprocess_forestplots:
    run: stata-mp:latest analysis/model_forestplots.do
    needs: [andescriptives_models]
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_*.svg 

  anprocess_forestplots_CoxR2:
    run: stata-mp:latest analysis/an_processout_regressionmodels_FOREST_R2.do
    needs: [ancoxMI]
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_regressionmodels_FOREST_R2_COX.svg 

  anprocess_forestplots_CoxCauseSpecificR2:
    run: stata-mp:latest analysis/an_processout_coxcausespecific_R2_FOREST.do
    needs: 
      - anCOXr2circulatory
      - anCOXr2cancer_ex_nmsc 
      - anCOXr2respiratory
      - anCOXr2respiratorylrti
      - anCOXr2digestive
      - anCOXr2mentalhealth
      - anCOXr2nervoussystem
      - anCOXr2genitourinary
      - anCOXr2endo_nutr_metabol
      - anCOXr2external
      - anCOXr2musculoskeletal
      - anCOXr2otherinfections
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_coxcausespecific_R2_FOREST.svg 


  anprocess_forestplots_FG:
    run: stata-mp:latest analysis/an_processout_FGcausespecific_FOREST_R2.do
    needs: 
      - anFGcirculatory
      - anFGcancer_ex_nmsc 
      - anFGrespiratory
      - anFGrespiratorylrti
      - anFGdigestive
      - anFGmentalhealth
      - anFGnervoussystem
      - anFGgenitourinary
      - anFGendo_nutr_metabol
      - anFGexternal
      - anFGmusculoskeletal
      - anFGotherinfections
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_FGcausespecific_R2_FOREST.svg 

  anprocess_forestplots_coxbytime:
    run: stata-mp:latest analysis/an_processout_coxbytime_FOREST.do
    needs: 
      - ancoxbytime
      - anCOXr2bytimecirculatory
      - anCOXr2bytimecancer_ex_nmsc 
      - anCOXr2bytimerespiratory
      - anCOXr2bytimerespiratorylrti
      - anCOXr2bytimedigestive
      - anCOXr2bytimementalhealth
      - anCOXr2bytimenervoussystem
      - anCOXr2bytimegenitourinary
      - anCOXr2bytimeendo_nutr_metabol
      - anCOXr2bytimeexternal
      - anCOXr2bytimemusculoskeletal
      - anCOXr2bytimeotherinfections
    outputs:
      moderately_sensitive:
        graphs: analysis/output/an_processout_coxbytime_FOREST.svg 

  anphchecks:
    run: stata-mp:latest analysis/an_phchecks.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_phchecks.log

  ansensanal:
    run: stata-mp:latest analysis/an_sensanalyses.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_senseanalyses.log


  an_SAcirculatory:
    run: stata-mp:latest analysis/an_SAcausespecific.do circulatory 345
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificcirculatory.log
        models: analysis/output/models/an_SAcausespecificcirculatory*.ster

  an_SAcancer_ex_nmsc:
    run: stata-mp:latest analysis/an_SAcausespecific.do cancer_ex_nmsc 6266
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificcancer_ex_nmsc.log
        models: analysis/output/models/an_SAcausespecificcancer_ex_nmsc*.ster

  an_SArespiratory:
    run: stata-mp:latest analysis/an_SAcausespecific.do respiratory 7883
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificrespiratory.log
        models: analysis/output/models/an_SAcausespecificrespiratory*.ster

  an_SArespiratorylrti:
    run: stata-mp:latest analysis/an_SAcausespecific.do respiratorylrti 40905
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificrespiratorylrti.log
        models: analysis/output/models/an_SAcausespecificrespiratorylrti*.ster

  an_SAdigestive:
    run: stata-mp:latest analysis/an_SAcausespecific.do digestive 3985
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificdigestive.log
        models: analysis/output/models/an_SAcausespecificdigestive*.ster

  an_SAmentalhealth:
    run: stata-mp:latest analysis/an_SAcausespecific.do mentalhealth 347
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificmentalhealth.log
        models: analysis/output/models/an_SAcausespecificmentalhealth*.ster

  an_SAnervoussystem:
    run: stata-mp:latest analysis/an_SAcausespecific.do nervoussystem 23
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificnervoussystem.log
        models: analysis/output/models/an_SAcausespecificnervoussystem*.ster

  an_SAgenitourinary:
    run: stata-mp:latest analysis/an_SAcausespecific.do genitourinary 4556
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificgenitourinary.log
        models: analysis/output/models/an_SAcausespecificgenitourinary*.ster

  an_SAendo_nutr_metabol:
    run: stata-mp:latest analysis/an_SAcausespecific.do endo_nutr_metabol 5995
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificendo_nutr_metabol.log
        models: analysis/output/models/an_SAcausespecificendo_nutr_metabol*.ster

  an_SAexternal:
    run: stata-mp:latest analysis/an_SAcausespecific.do external 2068
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificexternal.log
        models: analysis/output/models/an_SAcausespecificexternal*.ster

  an_SAmusculoskeletal:
    run: stata-mp:latest analysis/an_SAcausespecific.do musculoskeletal 92885
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificmusculoskeletal.log
        models: analysis/output/models/an_SAcausespecificmusculoskeletal*.ster

  an_SAotherinfections:
    run: stata-mp:latest analysis/an_SAcausespecific.do otherinfections 158
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_SAcausespecificotherinfections.log
        models: analysis/output/models/an_SAcausespecificotherinfections*.ster


  runsingledofile:
    run: stata-mp:latest analysis/an_descriptive.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        log: analysis/output/an_descriptive.log
        table: analysis/output/an_descriptive_OUTCOMES.txt
        histogram: analysis/output/an_descriptive_EVENTSBYTIME.svg

  rundescriptivetablealone:
    run: stata-mp:latest analysis/an_desctable.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        tables: analysis/output/an_desctable*.txt

  runKMsalone:
    run: stata-mp:latest analysis/an_cumulativeincidence.do
    needs: [appenddata]
    outputs:
      moderately_sensitive:
        kmcis: analysis/output/an_cumulativeinc*.svg
    

  run_model:
    run: stata-mp:latest analysis/model.do
    needs: [generate_study_pop_covdischarged]
    outputs:
      moderately_sensitive:
        log: logs/model.log

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Krishnan Bhaskaran
Branch
master
Force run dependencies
No
Git commit hash
d4a589b
Requested actions
  • an_SAcancer_ex_nmsc
  • an_SArespiratory
  • an_SArespiratorylrti