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Job request: 13487

Workspace:
post-covid-pre-vaccinated-cardiovascular
ID:
pwpeqlifnvjkd47t

This page shows the technical details of what happened when authorised researcher Rochelle Knight 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:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  preprocess_data:
    run: r:latest analysis/preprocess/preprocess_data.R
    needs:
    - generate_study_population
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_stage0.txt
      highly_sensitive:
        cohort: output/input.rds
        venn: output/venn.rds

  stage1_data_cleaning:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R
    needs:
    - preprocess_data
    outputs:
      moderately_sensitive:
        QA_rules: output/review/descriptives/QA_summary.csv
        refactoring: output/not-for-review/meta_data_factors.csv
        IE_criteria: output/review/descriptives/cohort_flow.csv
        histograms: output/not-for-review/numeric_histograms.svg
      highly_sensitive:
        cohort: output/input_stage1.rds

  stage1_end_date_table:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates.rds

  stage2_missing_table1:
    run: r:latest analysis/descriptives/Stage2_Missing_Table1.R
    needs:
    - stage1_data_cleaning
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/not-for-review/Check_missing_range.csv
        DateChecks: output/not-for-review/Check_dates_range.csv
        Descriptive_Table: output/review/descriptives/Table1_pre_vaccination_cvd.csv

  table_2:
    run: r:latest analysis/descriptives/table_2.R
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        table_2: output/review/descriptives/table2_pre_vaccination_cvd.csv

  venn_diagram:
    run: r:latest analysis/descriptives/venn_diagram.R
    needs:
    - preprocess_data
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*

  event_counts_by_time_period:
    run: r:latest analysis/descriptives/event_counts_by_time_period.R
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        event_counts: output/review/descriptives/event_counts_by_time_period_pre_vaccination.csv

  ## Apply cox model for ami 

  Analysis_cox_ami:
    run: r:latest analysis/model/01_cox_pipeline.R ami
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ami_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ami_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_isch 

  Analysis_cox_stroke_isch:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_isch_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_isch_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for dvt 

  Analysis_cox_dvt:
    run: r:latest analysis/model/01_cox_pipeline.R dvt
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_dvt_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_dvt_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for pe 

  Analysis_cox_pe:
    run: r:latest analysis/model/01_cox_pipeline.R pe
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_pe_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_pe_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for tia 

  Analysis_cox_tia:
    run: r:latest analysis/model/01_cox_pipeline.R tia
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_tia_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_tia_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_sah_hs 

  Analysis_cox_stroke_sah_hs:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_sah_hs_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_sah_hs_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for hf 

  Analysis_cox_hf:
    run: r:latest analysis/model/01_cox_pipeline.R hf
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_hf_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_hf_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for angina 

  Analysis_cox_angina:
    run: r:latest analysis/model/01_cox_pipeline.R angina
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_angina_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_angina_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ate 

  Analysis_cox_ate:
    run: r:latest analysis/model/01_cox_pipeline.R ate
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ate_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ate_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for vte 

  Analysis_cox_vte:
    run: r:latest analysis/model/01_cox_pipeline.R vte
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_vte_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_vte_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ami_primary_position 

  Analysis_cox_ami_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ami_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ami_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_isch_primary_position 

  Analysis_cox_stroke_isch_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_isch_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_isch_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for dvt_primary_position 

  Analysis_cox_dvt_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_dvt_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_dvt_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for pe_primary_position 

  Analysis_cox_pe_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_pe_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_pe_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for tia_primary_position 

  Analysis_cox_tia_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_tia_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_tia_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for stroke_sah_hs_primary_position 

  Analysis_cox_stroke_sah_hs_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_stroke_sah_hs_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_stroke_sah_hs_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for hf_primary_position 

  Analysis_cox_hf_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_hf_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_hf_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for angina_primary_position 

  Analysis_cox_angina_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_angina_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_angina_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for ate_primary_position 

  Analysis_cox_ate_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_ate_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_ate_primary_position_*_pre_vaccination_*_time_periods.csv

  ## Apply cox model for vte_primary_position 

  Analysis_cox_vte_primary_position:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position
    needs:
    - stage1_data_cleaning
    - stage1_end_date_table
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_pre_vaccination.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_pre_vaccination.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_pre_vaccination_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_pre_vaccination.csv
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_pre_vaccination.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_time_periods.txt
      highly_sensitive:
        sampled_data: output/input_sampled_data_vte_primary_position_*_pre_vaccination_*_time_periods.csv
        cox_input_data: output/input_vte_primary_position_*_pre_vaccination_*_time_periods.csv

  stata_cox_model_ami_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_tia_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_tia_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_sah_hs
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ami_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_stroke_isch_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_dvt_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_pe_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_tia_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_hf_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_angina_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_ate_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte_primary_position
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_agegp_60_79_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_agegp_60_79_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_ethnicity_Other_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_ethnicity_Other_pre_vaccination_reduced_time_periods_cox_model.txt

  stata_cox_model_vte_aer_Male_60_79_pre_vaccination_reduced:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods
    needs:
    - Analysis_cox_vte
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods_stata_median_fup.csv
        stata_output: output/input_sampled_data_vte_aer_Male_60_79_pre_vaccination_reduced_time_periods_cox_model.txt

  format_stata_output:
    run: r:latest analysis/format_stata_output.R
    needs:
    - stata_cox_model_ami_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_stroke_isch_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_dvt_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_pe_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_tia_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_stroke_sah_hs_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_hf_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_angina_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_ate_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_vte_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_ami_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_stroke_isch_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_dvt_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_pe_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_tia_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_hf_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_angina_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_ate_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_vte_primary_position_covid_pheno_hospitalised_pre_vaccination_reduced
    - stata_cox_model_vte_agegp_60_79_pre_vaccination_reduced
    - stata_cox_model_vte_ethnicity_Other_pre_vaccination_reduced
    - stata_cox_model_vte_aer_Male_60_79_pre_vaccination_reduced
    outputs:
      moderately_sensitive:
        stata_output: output/stata_output.csv

Timeline

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Job information

Status
Succeeded
Backend
TPP
Requested by
Rochelle Knight
Branch
main
Force run dependencies
No
Git commit hash
67cbfc9
Requested actions
  • Analysis_cox_ami
  • Analysis_cox_stroke_isch
  • Analysis_cox_dvt
  • Analysis_cox_pe
  • Analysis_cox_tia
  • Analysis_cox_stroke_sah_hs
  • Analysis_cox_hf
  • Analysis_cox_angina
  • Analysis_cox_ate
  • Analysis_cox_vte
  • Analysis_cox_ami_primary_position
  • Analysis_cox_stroke_isch_primary_position
  • Analysis_cox_dvt_primary_position
  • Analysis_cox_pe_primary_position
  • Analysis_cox_tia_primary_position
  • Analysis_cox_stroke_sah_hs_primary_position
  • Analysis_cox_hf_primary_position
  • Analysis_cox_angina_primary_position
  • Analysis_cox_ate_primary_position
  • Analysis_cox_vte_primary_position