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Job request: 16736

Organisation:
University of Manchester
Workspace:
sepsis_hosp_admission
ID:
7vxa3n2uwbsqlpzf

This page shows the technical details of what happened when authorised researcher Billy Zhong 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: 30000

actions:

### study cohort ###
  generate_study_population_case:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case
    outputs:
      highly_sensitive:
        cohort: output/input_case.csv

  generate_study_population_case_test:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_test
    outputs:
      highly_sensitive:
        cohort: output/input_case_test.csv

  generate_study_population_control_1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_1
    outputs:
      highly_sensitive:
        cohort: output/input_control_1.csv

  generate_study_population_control_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_2
    outputs:
      highly_sensitive:
        cohort: output/input_control_2.csv

  generate_study_population_control_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_3
    outputs:
      highly_sensitive:
        cohort: output/input_control_3.csv

  generate_study_population_control_4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_4
    outputs:
      highly_sensitive:
        cohort: output/input_control_4.csv

  generate_study_population_control_5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_5
    outputs:
      highly_sensitive:
        cohort: output/input_control_5.csv

  generate_study_population_control_6:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_6
    outputs:
      highly_sensitive:
        cohort: output/input_control_6.csv

  generate_study_population_control_7:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_7
    outputs:
      highly_sensitive:
        cohort: output/input_control_7.csv

  generate_study_population_control_8:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_8
    outputs:
      highly_sensitive:
        cohort: output/input_control_8.csv

  case_check:  
    run: r:latest analysis/case_check.R
    needs: [generate_study_population_case]
    outputs:
      highly_sensitive:
        cohort: output/case_ch.csv
      moderately_sensitive:
        table1: output/case_check.csv
        table2: output/case_frequency_check.csv

  sepsis_trend:  
    run: r:latest analysis/sepsis_trend.R
    needs: [case_check]
    outputs:
      moderately_sensitive:
        plot1: output/figure_2.1.jpeg
        plot2: output/figure_2.2.jpeg
        plot3: output/figure_2.3.jpeg
        table1: output/figure_2.3_table.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-12-31 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  sepsis_trend_rate:  
    run: r:latest analysis/sepsis_trend_rate.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate.jpeg
        table1: output/figure_rate_table.csv

  sepsis_trend_rate_com:  
    run: r:latest analysis/sepsis_trend_rate_com.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate_com.jpeg

  sepsis_trend_rate_hos:  
    run: r:latest analysis/sepsis_trend_rate_hos.R
    needs: [case_check,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate_hos.jpeg

  process1:  
    run: r:latest analysis/process1.R
    needs: [case_check,generate_study_population_control_1,generate_study_population_control_2,
    generate_study_population_control_3,generate_study_population_control_4,generate_study_population_control_5,
    generate_study_population_control_6,generate_study_population_control_7,generate_study_population_control_8]
    outputs:
      highly_sensitive:
        cohort1: output/case_191.csv
        cohort2: output/case_192.csv
        cohort3: output/case_201.csv
        cohort4: output/case_202.csv
        cohort5: output/case_211.csv
        cohort6: output/case_212.csv
        cohort7: output/case_221.csv
        cohort8: output/case_222.csv
        cohort9: output/control_191.csv
        cohort10: output/control_192.csv
        cohort11: output/control_201.csv
        cohort12: output/control_202.csv
        cohort13: output/control_211.csv
        cohort14: output/control_212.csv
        cohort15: output/control_221.csv
        cohort16: output/control_222.csv

  matching1:
    run: python:latest python analysis/matching1.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_191.csv
        table2: output/matched_matches_191.csv
        table3: output/matched_combined_191.csv
        table4: output/matched_cases_192.csv
        table5: output/matched_matches_192.csv
        table6: output/matched_combined_192.csv
      moderately_sensitive: 
        report1: output/matching_report_191.txt
        report2: output/matching_report_192.txt

  matching2:
    run: python:latest python analysis/matching2.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_201.csv
        table2: output/matched_matches_201.csv
        table3: output/matched_combined_201.csv
        table4: output/matched_cases_202.csv
        table5: output/matched_matches_202.csv
        table6: output/matched_combined_202.csv
      moderately_sensitive: 
        report1: output/matching_report_201.txt
        report2: output/matching_report_202.txt

  matching3:
    run: python:latest python analysis/matching3.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_211.csv
        table2: output/matched_matches_211.csv
        table3: output/matched_combined_211.csv
        table4: output/matched_cases_212.csv
        table5: output/matched_matches_212.csv
        table6: output/matched_combined_212.csv
      moderately_sensitive: 
        report1: output/matching_report_211.txt
        report2: output/matching_report_212.txt

  matching4:
    run: python:latest python analysis/matching4.py
    needs: [process1]
    outputs:
      highly_sensitive: 
        table1: output/matched_cases_221.csv
        table2: output/matched_matches_221.csv
        table3: output/matched_combined_221.csv
      moderately_sensitive: 
        report1: output/matching_report_221.txt


  process_covidinclude:  
    run: r:latest analysis/process_covidinclude.R
    needs: [generate_study_population_case]
    outputs:
      highly_sensitive:
        cohort: output/case_covidinclude.csv
      moderately_sensitive:
        table1: output/case_frequency_check1.csv
        table2: output/case_frequency_check2.csv

  sepsis_trend_rate_covidinclude:  
    run: r:latest analysis/sepsis_trend_rate_covidinclude.R
    needs: [process_covidinclude,generate_measures]
    outputs:
      moderately_sensitive:
        plot1: output/figure_rate_covidinclude.jpeg
        table1: output/figure_rate_covidinclude_table.csv
        plot2: output/figure_rate_covidinclude_com.jpeg
        plot3: output/figure_rate_covidinclude_hos.jpeg

  process_noexclude:  
    run: r:latest analysis/process_noexclude.R
    needs: [generate_study_population_case]
    outputs:
      moderately_sensitive:
        plot1: output/figure_noexclude.jpeg
        table1: output/figure_noexclude_table.csv

  process2_idextraction:  
    run: r:latest analysis/process2_idextraction.R
    needs: [matching1,matching2,matching3,matching4]
    outputs:
      highly_sensitive:
        cohort: output/case_id.csv

  generate_study_population_variables:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_variables
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_variables.csv

  process3_idextraction:  
    run: r:latest analysis/process3_idextraction.R
    needs: [matching1,matching2,matching3,matching4]
    outputs:
      highly_sensitive:
        cohort1: output/control_id_191.csv
        cohort2: output/control_id_192.csv
        cohort3: output/control_id_201.csv
        cohort4: output/control_id_202.csv
        cohort5: output/control_id_211.csv
        cohort6: output/control_id_212.csv
        cohort7: output/control_id_221.csv

  generate_study_population_control_var_191:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_191.csv

  generate_study_population_control_var_192:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_192.csv

  generate_study_population_control_var_201:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_201.csv

  generate_study_population_control_var_202:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_202.csv

  generate_study_population_control_var_211:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_211.csv

  generate_study_population_control_var_212:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_212.csv

  generate_study_population_control_var_221:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_221.csv

  process_data:
    run: r:latest analysis/data_process.R
    needs: [generate_study_population_variables]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_case_data.rds

  process_data_control:
    run: r:latest analysis/data_process_control.R
    needs: [generate_study_population_control_var_191,generate_study_population_control_var_192,
    generate_study_population_control_var_201,generate_study_population_control_var_202,
    generate_study_population_control_var_211,generate_study_population_control_var_212,
    generate_study_population_control_var_221]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_control_data.rds

# Skim data
  skim_data_case:
    run: r:latest analysis/data_skim.R output/processed/input_case_data.rds output/data_properties
    needs: [process_data]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_case_data_skim.txt
        txt2: output/data_properties/input_case_data_coltypes.txt
        txt3: output/data_properties/input_case_data_tabulate.txt

  skim_data_control:
    run: r:latest analysis/data_skim.R output/processed/input_control_data.rds output/data_properties
    needs: [process_data_control]
    outputs: 
      moderately_sensitive:
        txt1: output/data_properties/input_control_data_skim.txt
        txt2: output/data_properties/input_control_data_coltypes.txt
        txt3: output/data_properties/input_control_data_tabulate.txt

  extract_case_ab_6w: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ab
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_case_ab.csv

  extract_control_ab_6w_191: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_191.csv

  extract_control_ab_6w_192: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_192.csv

  extract_control_ab_6w_201: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_201.csv

  extract_control_ab_6w_202: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_202.csv

  extract_control_ab_6w_211: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_211.csv

  extract_control_ab_6w_212: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_212.csv

  extract_control_ab_6w_221: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_221.csv

  process_ab_case:
    run: r:latest analysis/process_ab_case.R
    needs: [extract_case_ab_6w]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_case_ab.rds

  process_ab_control:
    run: r:latest analysis/process_ab_control.R
    needs: [extract_control_ab_6w_191,extract_control_ab_6w_192,extract_control_ab_6w_201,
    extract_control_ab_6w_202,extract_control_ab_6w_211,extract_control_ab_6w_212,extract_control_ab_6w_221]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_control_ab.rds

  check_age_dist:  
    run: r:latest analysis/check_age_dist.R
    needs: [matching1,matching2,matching3,matching4]
    outputs:
      moderately_sensitive:
        plot1: output/case_18.jpeg

  extract_case_var_add:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_var_add
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_case_var_add.csv

  extract_case_var_add_191: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_191.csv

  extract_case_var_add_192: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_192.csv

  extract_case_var_add_201: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_201.csv

  extract_case_var_add_202: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_202.csv

  extract_case_var_add_211: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_211.csv

  extract_case_var_add_212: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_212.csv

  extract_case_var_add_221: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_var_add_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_var_add_221.csv

  process_model_var:
    run: r:latest analysis/process_model_var.R
    needs: [matching1,matching2,matching3,matching4,
    process_data,process_data_control,
    process_ab_case,process_ab_control,
    process_ab_case_6w,process_ab_control_6w,
    extract_case_var_add,extract_case_var_add_191,
    extract_case_var_add_192,extract_case_var_add_201,
    extract_case_var_add_202,extract_case_var_add_211,
    extract_case_var_add_212,extract_case_var_add_221]
    outputs:
      highly_sensitive: 
        rds1: output/processed/input_model_c_h.rds
        rds2: output/processed/input_model_c.rds
        rds3: output/processed/input_model_h.rds

  process_table_1:
    run: r:latest analysis/Table1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/table_1_case.csv
        table2: output/table_1_control.csv

  process_table_1_separate:
    run: r:latest analysis/Table1_separate.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/table_1_case_com.csv
        table2: output/table_1_control_com.csv
        table3: output/table_1_case_hos.csv
        table4: output/table_1_control_hos.csv

  process_table_1_byimd:
    run: r:latest analysis/Table1_byimd.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/table_1_imd1_case.csv
        table2: output/table_1_imd2_case.csv
        table3: output/table_1_imd3_case.csv
        table4: output/table_1_imd4_case.csv
        table5: output/table_1_imd5_case.csv
        table6: output/table_1_imd1_control.csv
        table7: output/table_1_imd2_control.csv
        table8: output/table_1_imd3_control.csv
        table9: output/table_1_imd4_control.csv
        table10: output/table_1_imd5_control.csv

  model_crude_ch:
    run: r:latest analysis/model_crude_ch.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch.rds

  model_crude_c:
    run: r:latest analysis/model_crude_c.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c.rds

  model_crude_h:
    run: r:latest analysis/model_crude_h.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h.rds

  model_crude_plot:
    run: r:latest analysis/model_crude_plot.R
    needs: [model_crude_h,model_crude_c,model_crude_ch]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota.csv
        table2: output/crude_plotb.csv

  Figure_2A_crude:  
    run: r:latest analysis/Figure_2A_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2A_crude_1.jpeg
        plot2: output/Figure_2A_crude_2.jpeg

  Figure_2B_crude:  
    run: r:latest analysis/Figure_2B_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2B_crude.jpeg

  Figure_2C_crude:  
    run: r:latest analysis/Figure_2C_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2C_crude.jpeg

  Figure_2D_crude:  
    run: r:latest analysis/Figure_2D_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2D_crude.jpeg

  Figure_2E_crude:  
    run: r:latest analysis/Figure_2E_crude.R
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2E_crude.jpeg

  model_adjusted_plot:
    run: r:latest analysis/model_adjusted_plot.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_plotimd.csv
        table1: output/adjusted_plota.csv
        table2: output/adjusted_plotb.csv
        table3: output/adjusted_plotc.csv
        table4: output/adjusted_plotd.csv
        table5: output/adjusted_plote.csv

  Figure_2A:  
    run: r:latest analysis/Figure_2A.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2A_adjusted_1.jpeg
        plot2: output/Figure_2A_adjusted_2.jpeg

  Figure_2B:  
    run: r:latest analysis/Figure_2B.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2B_adjusted.jpeg

  Figure_2C:  
    run: r:latest analysis/Figure_2C.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2C_adjusted.jpeg

  Figure_2D:  
    run: r:latest analysis/Figure_2D.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2D_adjusted.jpeg

  Figure_2E:  
    run: r:latest analysis/Figure_2E.R
    needs: [model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2E_adjusted.jpeg

  model_adjusted_plot_type:
    run: r:latest analysis/model_adjusted_plot_type.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_type_plotimd.csv
        table1: output/adjusted_type_plota.csv
        table2: output/adjusted_type_plotb.csv
        table3: output/adjusted_type_plotc.csv
        table4: output/adjusted_type_plotd.csv
        table5: output/adjusted_type_plote.csv

  Figure_2E_type:  
    run: r:latest analysis/Figure_2E_type.R
    needs: [model_adjusted_plot_type]
    outputs:
      moderately_sensitive:
        plot2: output/Figure_2E_adjusted_type.jpeg

  model_imd:
    run: r:latest analysis/model_imd.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/imd_model.csv
        table2: output/imd_model_covid.csv
        table3: output/imd_model_cardiometabolic.csv
        
  Figure_2_IMD:  
    run: r:latest analysis/Figure_2_IMD.R
    needs: [model_imd]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2_IMD.jpeg

  Figure_2_IMD_crude:  
    run: r:latest analysis/Figure_2_IMD_crude.R
    needs: [model_imd]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2_IMD_crude.jpeg

  Figure_2_IMD_combine:  
    run: r:latest analysis/Figure_2_IMD_combine.R
    needs: [model_imd,model_adjusted_plot]
    outputs:
      moderately_sensitive:
        plot1: output/Figure_2_IMD_combine.jpeg

  mortality_rate:
    run: r:latest analysis/mortality_rate.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/model_mortality.csv

  mortality_model_time:
    run: r:latest analysis/mortality_model_time.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/model_mortality_1.csv
        table2: output/model_mortality_2.csv
        table3: output/model_mortality_3.csv
        table4: output/model_mortality_all.csv

  plot_mortality_model:
    run: r:latest -e 'rmarkdown::render("analysis/mortality_model_plot.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [mortality_model_time]
    outputs:
      moderately_sensitive:
        csv: output/mortality_model_plot.html

  mortality_table:
    run: r:latest analysis/mortality_table.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/mortality_table_all.csv
        table2: output/mortality_table_c.csv
        table3: output/mortality_table_h.csv

  age_check:
    run: r:latest analysis/age_check.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        plot1: output/age_check_1.jpeg
        plot2: output/age_check_2.jpeg

  model_adjusted_clinical:
    run: r:latest analysis/model_adjusted_clinical.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1.csv
        table1: output/adjusted_clinical_2.csv
        table2: output/adjusted_clinical_3.csv

  Figure_adjusted_clinical:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical.html

  Figure_crude_demo:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo.html

  Figure_crude_clinical:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical.html

### adjusted model in period 1/2/3 ###
  model_adjusted_clinical_period_1:
    run: r:latest analysis/model_adjusted_clinical_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1_period_1.csv
        table1: output/adjusted_clinical_2_period_1.csv
        table2: output/adjusted_clinical_3_period_1.csv

  model_adjusted_clinical_period_2:
    run: r:latest analysis/model_adjusted_clinical_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1_period_2.csv
        table1: output/adjusted_clinical_2_period_2.csv
        table2: output/adjusted_clinical_3_period_2.csv

  model_adjusted_clinical_period_3:
    run: r:latest analysis/model_adjusted_clinical_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/adjusted_clinical_1_period_3.csv
        table1: output/adjusted_clinical_2_period_3.csv
        table2: output/adjusted_clinical_3_period_3.csv

  Figure_adjusted_clinical_period_1:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical_period_1]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical_period_1.html

  Figure_adjusted_clinical_period_2:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical_period_2]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical_period_2.html

  Figure_adjusted_clinical_period_3:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_adjusted_clinical_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_adjusted_clinical_period_3]
    outputs:
      moderately_sensitive:
        csv: output/Figure_adjusted_clinical_period_3.html

### crude model in period 1/2/3 ###
  model_crude_ch_period_1:
    run: r:latest analysis/model_crude_ch_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_period_1.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch_period_1.rds

  model_crude_ch_period_2:
    run: r:latest analysis/model_crude_ch_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_period_2.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch_period_2.rds

  model_crude_ch_period_3:
    run: r:latest analysis/model_crude_ch_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_period_3.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_ch_period_3.rds

  model_crude_c_period_1:
    run: r:latest analysis/model_crude_c_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c_period_1.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c_period_1.rds

  model_crude_c_period_2:
    run: r:latest analysis/model_crude_c_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c_period_2.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c_period_2.rds

  model_crude_c_period_3:
    run: r:latest analysis/model_crude_c_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_c_period_3.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_c_period_3.rds

  model_crude_h_period_1:
    run: r:latest analysis/model_crude_h_period_1.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h_period_1.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h_period_1.rds

  model_crude_h_period_2:
    run: r:latest analysis/model_crude_h_period_2.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h_period_2.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h_period_2.rds

  model_crude_h_period_3:
    run: r:latest analysis/model_crude_h_period_3.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table1: output/crude_model_result_h_period_3.csv
      highly_sensitive: 
        rds1: output/processed/input_crude_model_h_period_3.rds

  model_crude_plot_period_1:
    run: r:latest analysis/model_crude_plot_period_1.R
    needs: [model_crude_h_period_1,model_crude_c_period_1,model_crude_ch_period_1]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota_period_1.csv
        table2: output/crude_plotb_period_1.csv

  model_crude_plot_period_2:
    run: r:latest analysis/model_crude_plot_period_2.R
    needs: [model_crude_h_period_2,model_crude_c_period_2,model_crude_ch_period_2]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota_period_2.csv
        table2: output/crude_plotb_period_2.csv

  model_crude_plot_period_3:
    run: r:latest analysis/model_crude_plot_period_3.R
    needs: [model_crude_h_period_3,model_crude_c_period_3,model_crude_ch_period_3]
    outputs:
      moderately_sensitive:
        table1: output/crude_plota_period_3.csv
        table2: output/crude_plotb_period_3.csv

  Figure_crude_clinical_period_1:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_1]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical_period_1.html

  Figure_crude_clinical_period_2:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_2]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical_period_2.html

  Figure_crude_clinical_period_3:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_clinical_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_3]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_clinical_period_3.html

  Figure_crude_demo_period_1:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_1.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_1]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo_period_1.html

  Figure_crude_demo_period_2:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_2.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_2]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo_period_2.html

  Figure_crude_demo_period_3:
    run: r:latest -e 'rmarkdown::render("analysis/Figure_crude_demo_period_3.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [model_crude_plot_period_3]
    outputs:
      moderately_sensitive:
        csv: output/Figure_crude_demo_period_3.html
### extract ab from -42days to index date
  extract_case_ab_in6w: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_case_ab_6w
    needs: [process2_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_case_ab_6w.csv

  extract_control_ab_in6w_191: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_191
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_191.csv

  extract_control_ab_in6w_192: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_192
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_192.csv

  extract_control_ab_in6w_201: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_201
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_201.csv

  extract_control_ab_in6w_202: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_202
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_202.csv

  extract_control_ab_in6w_211: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_211
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_211.csv

  extract_control_ab_in6w_212: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_212
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_212.csv

  extract_control_ab_in6w_221: 
    run: cohortextractor:latest generate_cohort --study-definition study_definition_control_ab_6w_221
    needs: [process3_idextraction]
    outputs:
      highly_sensitive:
        cohort: output/input_control_ab_6w_221.csv

  process_ab_case_6w:
    run: r:latest analysis/process_ab_case_6w.R
    needs: [extract_case_ab_in6w]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_case_ab_6w.rds

  process_ab_control_6w:
    run: r:latest analysis/process_ab_control_6w.R
    needs: [extract_control_ab_in6w_191,extract_control_ab_in6w_192,extract_control_ab_in6w_201,
    extract_control_ab_in6w_202,extract_control_ab_in6w_211,extract_control_ab_in6w_212,extract_control_ab_in6w_221]
    outputs:
      highly_sensitive: 
        rds: output/processed/input_control_ab_6w.rds

##### sensitivity #####

##### antibiotic use within six weeks #####
  sen_adjusted_clinical_ab_6w:
    run: r:latest analysis/sensitivity/sen_adjusted_clinical_ab_6w.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/sen_adjusted_clinical_ab_6w_1.csv
        table1: output/sen_adjusted_clinical_ab_6w_2.csv
        table2: output/sen_adjusted_clinical_ab_6w_3.csv

  Figure_sen_adjusted_clinical_ab_6w:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_sen_adjusted_clinical_ab_6w.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [sen_adjusted_clinical_ab_6w]
    outputs:
      moderately_sensitive:
        csv: output/Figure_sen_adjusted_clinical_ab_6w.html

  sen_crude_ab_6w:
    run: r:latest analysis/sensitivity/sen_crude_ab_6w.R
    needs: [process_model_var]
    outputs:
      moderately_sensitive:
        table6: output/sen_crude_ab_6w_plot.csv

  Figure_sen_crude_ab_6w:
    run: r:latest -e 'rmarkdown::render("analysis/sensitivity/Figure_sen_crude_ab_6w.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [sen_crude_ab_6w]
    outputs:
      moderately_sensitive:
        csv: output/Figure_sen_crude_ab_6w.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:37

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

Job information

Status
Succeeded
Backend
TPP
Requested by
Billy Zhong
Branch
sepsis
Force run dependencies
No
Git commit hash
54438da
Requested actions
  • Figure_sen_adjusted_clinical_ab_6w
  • Figure_sen_crude_ab_6w