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Job request: 9888

Workspace:
post-covid-vaccinated
ID:
cd437sygvmievbt6
View repo View project.yaml

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_electively_unvaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.feather

  generate_study_population_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.feather

  generate_study_population_index:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_index
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_index.feather

  preprocess_data_vaccinated:
    run: r:latest analysis/preprocess/preprocess_data.R vaccinated
    needs:
    - generate_study_population_index
    - generate_study_population_vaccinated
    - generate_study_population_electively_unvaccinated
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vaccinated_*.txt
        describe_index: output/not-for-review/describe_tmp_index_vaccinated.txt
        describe_cohort: output/not-for-review/describe_tmp_vaccinated.txt
        descrive_venn: output/not-for-review/describe_venn_vaccinated.txt
      highly_sensitive:
        cohort: output/input_vaccinated.rds
        venn: output/venn_vaccinated.rds

  preprocess_data_electively_unvaccinated:
    run: r:latest analysis/preprocess/preprocess_data.R electively_unvaccinated
    needs:
    - generate_study_population_index
    - generate_study_population_vaccinated
    - generate_study_population_electively_unvaccinated
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_electively_unvaccinated_*.txt
        describe_index: output/not-for-review/describe_tmp_index_electively_unvaccinated.txt
        describe_cohort: output/not-for-review/describe_tmp_electively_unvaccinated.txt
        descrive_venn: output/not-for-review/describe_venn_electively_unvaccinated.txt
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.rds
        venn: output/venn_electively_unvaccinated.rds

  stage1_data_cleaning_both:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R both
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_*.csv
        QA_rules: output/review/descriptives/QA_summary_*.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_vaccinated:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R vaccinated
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    - stage1_data_cleaning_both
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_vaccinated.rds

  stage1_end_date_table_electively_unvaccinated:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R electively_unvaccinated
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    - stage1_data_cleaning_both
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_electively_unvaccinated.rds

  stage2_missing_table1_both:
    run: r:latest analysis/descriptives/Stage2_missing_table1.R both
    needs:
    - stage1_data_cleaning_both
    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_*.csv

  stage3_diabetes_flow_vaccinated:
    run: r:latest analysis/descriptives/diabetes_flowchart.R vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_vaccinated.csv

  stage3_diabetes_flow_electively_unvaccinated:
    run: r:latest analysis/descriptives/diabetes_flowchart.R electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_electively_unvaccinated.csv

  ## Stage 4 - Table 2 - vaccinated cohort 

  stage4_table_2_vaccinated:
    run: r:latest analysis/descriptives/table_2.R vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_vaccinated.csv

  ## Stage 4 - Table 2 - electively_unvaccinated cohort 

  stage4_table_2_electively_unvaccinated:
    run: r:latest analysis/descriptives/table_2.R electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_electively_unvaccinated.csv

  stage4_venn_diagram_both:
    run: r:latest analysis/descriptives/venn_diagram.R both
    needs:
    - preprocess_data_vaccinated
    - preprocess_data_electively_unvaccinated
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*

  ## Cox model for ami - vaccinated 

  Analysis_cox_ami_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_vaccinated.csv

  ## Cox model for ami - electively_unvaccinated 

  Analysis_cox_ami_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_electively_unvaccinated.csv

  ## Cox model for stroke_isch - vaccinated 

  Analysis_cox_stroke_isch_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_vaccinated.csv

  ## Cox model for stroke_isch - electively_unvaccinated 

  Analysis_cox_stroke_isch_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_electively_unvaccinated.csv

  ## Cox model for dvt - vaccinated 

  Analysis_cox_dvt_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_vaccinated.csv

  ## Cox model for dvt - electively_unvaccinated 

  Analysis_cox_dvt_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_electively_unvaccinated.csv

  ## Cox model for pe - vaccinated 

  Analysis_cox_pe_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_vaccinated.csv

  ## Cox model for pe - electively_unvaccinated 

  Analysis_cox_pe_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_electively_unvaccinated.csv

  ## Cox model for tia - vaccinated 

  Analysis_cox_tia_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_vaccinated.csv

  ## Cox model for tia - electively_unvaccinated 

  Analysis_cox_tia_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_electively_unvaccinated.csv

  ## Cox model for stroke_sah_hs - vaccinated 

  Analysis_cox_stroke_sah_hs_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_vaccinated.csv

  ## Cox model for stroke_sah_hs - electively_unvaccinated 

  Analysis_cox_stroke_sah_hs_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_electively_unvaccinated.csv

  ## Cox model for hf - vaccinated 

  Analysis_cox_hf_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_vaccinated.csv

  ## Cox model for hf - electively_unvaccinated 

  Analysis_cox_hf_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_electively_unvaccinated.csv

  ## Cox model for angina - vaccinated 

  Analysis_cox_angina_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_vaccinated.csv

  ## Cox model for angina - electively_unvaccinated 

  Analysis_cox_angina_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_electively_unvaccinated.csv

  ## Cox model for ate - vaccinated 

  Analysis_cox_ate_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_vaccinated.csv

  ## Cox model for ate - electively_unvaccinated 

  Analysis_cox_ate_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_electively_unvaccinated.csv

  ## Cox model for vte - vaccinated 

  Analysis_cox_vte_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_vaccinated.csv

  ## Cox model for vte - electively_unvaccinated 

  Analysis_cox_vte_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_electively_unvaccinated.csv

  ## Cox model for ami_primary_position - vaccinated 

  Analysis_cox_ami_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_vaccinated.csv

  ## Cox model for ami_primary_position - electively_unvaccinated 

  Analysis_cox_ami_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ami_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ami_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ami_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ami_primary_position_electively_unvaccinated.csv

  ## Cox model for stroke_isch_primary_position - vaccinated 

  Analysis_cox_stroke_isch_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_vaccinated.csv

  ## Cox model for stroke_isch_primary_position - electively_unvaccinated 

  Analysis_cox_stroke_isch_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_isch_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_isch_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_isch_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated.csv

  ## Cox model for dvt_primary_position - vaccinated 

  Analysis_cox_dvt_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_vaccinated.csv

  ## Cox model for dvt_primary_position - electively_unvaccinated 

  Analysis_cox_dvt_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R dvt_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_dvt_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_dvt_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_dvt_primary_position_electively_unvaccinated.csv

  ## Cox model for pe_primary_position - vaccinated 

  Analysis_cox_pe_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_vaccinated.csv

  ## Cox model for pe_primary_position - electively_unvaccinated 

  Analysis_cox_pe_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R pe_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_pe_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_pe_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_pe_primary_position_electively_unvaccinated.csv

  ## Cox model for tia_primary_position - vaccinated 

  Analysis_cox_tia_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_vaccinated.csv

  ## Cox model for tia_primary_position - electively_unvaccinated 

  Analysis_cox_tia_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R tia_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_tia_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_tia_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_tia_primary_position_electively_unvaccinated.csv

  ## Cox model for stroke_sah_hs_primary_position - vaccinated 

  Analysis_cox_stroke_sah_hs_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
      vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_vaccinated.csv

  ## Cox model for stroke_sah_hs_primary_position - electively_unvaccinated 

  Analysis_cox_stroke_sah_hs_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R stroke_sah_hs_primary_position
      electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_stroke_sah_hs_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated.csv

  ## Cox model for hf_primary_position - vaccinated 

  Analysis_cox_hf_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_vaccinated.csv

  ## Cox model for hf_primary_position - electively_unvaccinated 

  Analysis_cox_hf_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R hf_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_hf_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_hf_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_hf_primary_position_electively_unvaccinated.csv

  ## Cox model for angina_primary_position - vaccinated 

  Analysis_cox_angina_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_vaccinated.csv

  ## Cox model for angina_primary_position - electively_unvaccinated 

  Analysis_cox_angina_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R angina_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_angina_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_angina_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_angina_primary_position_electively_unvaccinated.csv

  ## Cox model for ate_primary_position - vaccinated 

  Analysis_cox_ate_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_vaccinated.csv

  ## Cox model for ate_primary_position - electively_unvaccinated 

  Analysis_cox_ate_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R ate_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_ate_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_ate_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_ate_primary_position_electively_unvaccinated.csv

  ## Cox model for vte_primary_position - vaccinated 

  Analysis_cox_vte_primary_position_vaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_vaccinated.csv

  ## Cox model for vte_primary_position - electively_unvaccinated 

  Analysis_cox_vte_primary_position_electively_unvaccinated:
    run: r:latest analysis/model/01_cox_pipeline.R vte_primary_position electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    - select_covariates_for_hosp_covid
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/analyses_not_run_vte_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_vte_primary_position_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_vte_primary_position_electively_unvaccinated.csv

  split_hosp_covid_by_region_vaccinated:
    run: r:latest analysis/descriptives/hospitalised_covid_events_by_region.R vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        hosp_events_by_region_non_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_vaccinated_non_suppressed.csv
        hosp_events_by_region_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_vaccinated_suppressed.csv

  split_hosp_covid_by_region_electively_unvaccinated:
    run: r:latest analysis/descriptives/hospitalised_covid_events_by_region.R electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        hosp_events_by_region_non_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_electively_unvaccinated_non_suppressed.csv
        hosp_events_by_region_suppressed: output/not-for-review/hospitalised_covid_event_counts_by_region_electively_unvaccinated_suppressed.csv

  ## Hospitalised event counts by covariate - vaccinated 

  hosp_event_counts_by_covariate_level_vaccinated:
    run: r:latest analysis/descriptives/hospitalised_events_split_by_time_period_and_covariate_level.R
      vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        hosp_counts_by_covariate: output/not-for-review/hospitalised_event_counts_by_covariate_level_vaccinated.csv

  ## Hospitalised event counts by covariate - electively_unvaccinated 

  hosp_event_counts_by_covariate_level_electively_unvaccinated:
    run: r:latest analysis/descriptives/hospitalised_events_split_by_time_period_and_covariate_level.R
      electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        hosp_counts_by_covariate: output/not-for-review/hospitalised_event_counts_by_covariate_level_electively_unvaccinated.csv

  select_covariates_for_hosp_covid:
    run: r:latest analysis/descriptives/determine_covariates_for_hosp_covid.R both
    needs:
    - hosp_event_counts_by_covariate_level_vaccinated
    - hosp_event_counts_by_covariate_level_electively_unvaccinated
    outputs:
      moderately_sensitive:
        covariates_for_hosp_covid_vacc: output/not-for-review/covariates_to_adjust_for_hosp_covid_vaccinated.csv
        covariates_for_hosp_covid_electively_unvacc: output/not-for-review/covariates_to_adjust_for_hosp_covid_electively_unvaccinated.csv

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post-covid-vaccinated
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Rochelle Knight
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  • Analysis_cox_ami_electively_unvaccinated
  • Analysis_cox_dvt_electively_unvaccinated