Job request: 8450

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher RochelleKnight requested one or more actions to be run against real patient data in the post-covid-vaccinated 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

ID Status Action
wwzq2d2rdfgwmpvg succeeded Analysis_cox_angina_vaccinated

Pipeline

Show Hide 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_investigate:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_investigate
      --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_investigate.feather

  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

  investigation:
    run: r:latest analysis/investigation.R
    needs:
    - generate_study_population_investigate
    outputs:
      moderately_sensitive:
        describe: output/describe_input_investigate_*.txt

  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
      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:
      highly_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:
      highly_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_*

  ## Apply cox model for ami - vaccinated cohort 

  Analysis_cox_ami_vaccinated:
    run: r:latest analysis/model/01_pipe.R ami vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_ami_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_ami_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_ami_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_ami_vaccinated.csv

  ## Apply cox model for ami - electively_unvaccinated cohort 

  Analysis_cox_ami_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R ami electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_ami_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_ami_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_ami_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_ami_electively_unvaccinated.csv

  ## Apply cox model for stroke_isch - vaccinated cohort 

  Analysis_cox_stroke_isch_vaccinated:
    run: r:latest analysis/model/01_pipe.R stroke_isch vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_stroke_isch_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_stroke_isch_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_stroke_isch_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_stroke_isch_vaccinated.csv

  ## Apply cox model for stroke_isch - electively_unvaccinated cohort 

  Analysis_cox_stroke_isch_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R stroke_isch electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_stroke_isch_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_stroke_isch_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_stroke_isch_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_stroke_isch_electively_unvaccinated.csv

  ## Apply cox model for dvt - vaccinated cohort 

  Analysis_cox_dvt_vaccinated:
    run: r:latest analysis/model/01_pipe.R dvt vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_dvt_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_dvt_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_dvt_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_dvt_vaccinated.csv

  ## Apply cox model for dvt - electively_unvaccinated cohort 

  Analysis_cox_dvt_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R dvt electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_dvt_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_dvt_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_dvt_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_dvt_electively_unvaccinated.csv

  ## Apply cox model for pe - vaccinated cohort 

  Analysis_cox_pe_vaccinated:
    run: r:latest analysis/model/01_pipe.R pe vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_pe_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_pe_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_pe_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_pe_vaccinated.csv

  ## Apply cox model for pe - electively_unvaccinated cohort 

  Analysis_cox_pe_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R pe electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_pe_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_pe_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_pe_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_pe_electively_unvaccinated.csv

  ## Apply cox model for tia - vaccinated cohort 

  Analysis_cox_tia_vaccinated:
    run: r:latest analysis/model/01_pipe.R tia vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_tia_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_tia_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_tia_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_tia_vaccinated.csv

  ## Apply cox model for tia - electively_unvaccinated cohort 

  Analysis_cox_tia_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R tia electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_tia_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_tia_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_tia_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_tia_electively_unvaccinated.csv

  ## Apply cox model for stroke_sah_hs - vaccinated cohort 

  Analysis_cox_stroke_sah_hs_vaccinated:
    run: r:latest analysis/model/01_pipe.R stroke_sah_hs vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_stroke_sah_hs_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_stroke_sah_hs_vaccinated.csv

  ## Apply cox model for stroke_sah_hs - electively_unvaccinated cohort 

  Analysis_cox_stroke_sah_hs_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R stroke_sah_hs electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_stroke_sah_hs_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_stroke_sah_hs_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_stroke_sah_hs_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_stroke_sah_hs_electively_unvaccinated.csv

  ## Apply cox model for hf - vaccinated cohort 

  Analysis_cox_hf_vaccinated:
    run: r:latest analysis/model/01_pipe.R hf vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_hf_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_hf_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_hf_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_hf_vaccinated.csv

  ## Apply cox model for hf - electively_unvaccinated cohort 

  Analysis_cox_hf_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R hf electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_hf_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_hf_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_hf_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_hf_electively_unvaccinated.csv

  ## Apply cox model for angina - vaccinated cohort 

  Analysis_cox_angina_vaccinated:
    run: r:latest analysis/model/01_pipe.R angina vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_angina_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_angina_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_angina_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_angina_vaccinated.csv

  ## Apply cox model for angina - electively_unvaccinated cohort 

  Analysis_cox_angina_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R angina electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_angina_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_angina_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_angina_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_angina_electively_unvaccinated.csv

  ## Apply cox model for ate - vaccinated cohort 

  Analysis_cox_ate_vaccinated:
    run: r:latest analysis/model/01_pipe.R ate vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_ate_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_ate_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_ate_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_ate_vaccinated.csv

  ## Apply cox model for ate - electively_unvaccinated cohort 

  Analysis_cox_ate_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R ate electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_ate_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_ate_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_ate_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_ate_electively_unvaccinated.csv

  ## Apply cox model for vte - vaccinated cohort 

  Analysis_cox_vte_vaccinated:
    run: r:latest analysis/model/01_pipe.R vte vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_vte_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_vte_vaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_vte_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_vte_vaccinated.csv

  ## Apply cox model for vte - electively_unvaccinated cohort 

  Analysis_cox_vte_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R vte electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_vte_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_vte_electively_unvaccinated.html
        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
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_vte_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_vte_electively_unvaccinated.csv

  ## Apply cox model for depression - vaccinated cohort 

  Analysis_cox_depression_vaccinated:
    run: r:latest analysis/model/01_pipe.R depression vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_depression_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_depression_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_depression_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_depression_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_depression_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_depression_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_depression_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_depression_vaccinated.csv

  ## Apply cox model for depression - electively_unvaccinated cohort 

  Analysis_cox_depression_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R depression electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_depression_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_depression_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_depression_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_depression_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_depression_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_depression_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_depression_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_depression_electively_unvaccinated.csv

  ## Apply cox model for anxiety_general - vaccinated cohort 

  Analysis_cox_anxiety_general_vaccinated:
    run: r:latest analysis/model/01_pipe.R anxiety_general vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_anxiety_general_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_anxiety_general_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_anxiety_general_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_general_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_general_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_general_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_general_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_general_vaccinated.csv

  ## Apply cox model for anxiety_general - electively_unvaccinated cohort 

  Analysis_cox_anxiety_general_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R anxiety_general electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_anxiety_general_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_anxiety_general_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_anxiety_general_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_general_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_general_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_general_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_general_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_general_electively_unvaccinated.csv

  ## Apply cox model for anxiety_ocd - vaccinated cohort 

  Analysis_cox_anxiety_ocd_vaccinated:
    run: r:latest analysis/model/01_pipe.R anxiety_ocd vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_anxiety_ocd_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_anxiety_ocd_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_anxiety_ocd_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_ocd_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_ocd_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_ocd_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_ocd_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_ocd_vaccinated.csv

  ## Apply cox model for anxiety_ocd - electively_unvaccinated cohort 

  Analysis_cox_anxiety_ocd_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R anxiety_ocd electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_anxiety_ocd_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_anxiety_ocd_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_anxiety_ocd_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_ocd_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_ocd_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_ocd_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_ocd_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_ocd_electively_unvaccinated.csv

  ## Apply cox model for anxiety_ptsd - vaccinated cohort 

  Analysis_cox_anxiety_ptsd_vaccinated:
    run: r:latest analysis/model/01_pipe.R anxiety_ptsd vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_anxiety_ptsd_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_anxiety_ptsd_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_ptsd_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_ptsd_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_ptsd_vaccinated.csv

  ## Apply cox model for anxiety_ptsd - electively_unvaccinated cohort 

  Analysis_cox_anxiety_ptsd_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R anxiety_ptsd electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_anxiety_ptsd_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_anxiety_ptsd_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_anxiety_ptsd_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_anxiety_ptsd_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_anxiety_ptsd_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_anxiety_ptsd_electively_unvaccinated.csv

  ## Apply cox model for eating_disorders - vaccinated cohort 

  Analysis_cox_eating_disorders_vaccinated:
    run: r:latest analysis/model/01_pipe.R eating_disorders vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_eating_disorders_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_eating_disorders_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_eating_disorders_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_eating_disorders_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_eating_disorders_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_eating_disorders_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_eating_disorders_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_eating_disorders_vaccinated.csv

  ## Apply cox model for eating_disorders - electively_unvaccinated cohort 

  Analysis_cox_eating_disorders_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R eating_disorders electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_eating_disorders_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_eating_disorders_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_eating_disorders_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_eating_disorders_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_eating_disorders_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_eating_disorders_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_eating_disorders_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_eating_disorders_electively_unvaccinated.csv

  ## Apply cox model for serious_mental_illness - vaccinated cohort 

  Analysis_cox_serious_mental_illness_vaccinated:
    run: r:latest analysis/model/01_pipe.R serious_mental_illness vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_serious_mental_illness_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_serious_mental_illness_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_serious_mental_illness_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_serious_mental_illness_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_serious_mental_illness_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_serious_mental_illness_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_serious_mental_illness_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_serious_mental_illness_vaccinated.csv

  ## Apply cox model for serious_mental_illness - electively_unvaccinated cohort

    

  Analysis_cox_serious_mental_illness_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R serious_mental_illness electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_serious_mental_illness_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_serious_mental_illness_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_serious_mental_illness_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_serious_mental_illness_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_serious_mental_illness_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_serious_mental_illness_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_serious_mental_illness_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_serious_mental_illness_electively_unvaccinated.csv

  ## Apply cox model for self_harm_10plus - vaccinated cohort 

  Analysis_cox_self_harm_10plus_vaccinated:
    run: r:latest analysis/model/01_pipe.R self_harm_10plus vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_self_harm_10plus_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_self_harm_10plus_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_self_harm_10plus_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_self_harm_10plus_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_self_harm_10plus_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_self_harm_10plus_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_self_harm_10plus_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_self_harm_10plus_vaccinated.csv

  ## Apply cox model for self_harm_10plus - electively_unvaccinated cohort 

  Analysis_cox_self_harm_10plus_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R self_harm_10plus electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_self_harm_10plus_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_self_harm_10plus_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_self_harm_10plus_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_self_harm_10plus_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_self_harm_10plus_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_self_harm_10plus_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_self_harm_10plus_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_self_harm_10plus_electively_unvaccinated.csv

  ## Apply cox model for self_harm_15plus - vaccinated cohort 

  Analysis_cox_self_harm_15plus_vaccinated:
    run: r:latest analysis/model/01_pipe.R self_harm_15plus vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_self_harm_15plus_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_self_harm_15plus_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_self_harm_15plus_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_self_harm_15plus_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_self_harm_15plus_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_self_harm_15plus_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_self_harm_15plus_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_self_harm_15plus_vaccinated.csv

  ## Apply cox model for self_harm_15plus - electively_unvaccinated cohort 

  Analysis_cox_self_harm_15plus_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R self_harm_15plus electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_self_harm_15plus_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_self_harm_15plus_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_self_harm_15plus_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_self_harm_15plus_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_self_harm_15plus_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_self_harm_15plus_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_self_harm_15plus_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_self_harm_15plus_electively_unvaccinated.csv

  ## Apply cox model for suicide - vaccinated cohort 

  Analysis_cox_suicide_vaccinated:
    run: r:latest analysis/model/01_pipe.R suicide vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_suicide_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_suicide_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_suicide_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_suicide_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_suicide_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_suicide_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_suicide_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_suicide_vaccinated.csv

  ## Apply cox model for suicide - electively_unvaccinated cohort 

  Analysis_cox_suicide_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R suicide electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_suicide_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_suicide_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_suicide_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_suicide_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_suicide_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_suicide_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_suicide_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_suicide_electively_unvaccinated.csv

  ## Apply cox model for addiction - vaccinated cohort 

  Analysis_cox_addiction_vaccinated:
    run: r:latest analysis/model/01_pipe.R addiction vaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_addiction_vaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_addiction_vaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_addiction_vaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_addiction_vaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_addiction_vaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_addiction_vaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_addiction_vaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_addiction_vaccinated.csv

  ## Apply cox model for addiction - electively_unvaccinated cohort 

  Analysis_cox_addiction_electively_unvaccinated:
    run: r:latest analysis/model/01_pipe.R addiction electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    outputs:
      moderately_sensitive:
        compiled_hrs_html: output/review/model/suppressed_compiled_HR_results_addiction_electively_unvaccinated.html
        compiled_event_counts_html: output/review/model/suppressed_compiled_event_counts_addiction_electively_unvaccinated.html
        analyses_not_run: output/review/model/analyses_not_run_addiction_electively_unvaccinated.csv
        compiled_hrs_csv: output/review/model/suppressed_compiled_HR_results_addiction_electively_unvaccinated.csv
        compiled_hrs_csv_to_release: output/review/model/suppressed_compiled_HR_results_addiction_electively_unvaccinated_to_release.csv
        compiled_event_counts_csv: output/review/model/suppressed_compiled_event_counts_addiction_electively_unvaccinated.csv
      highly_sensitive:
        compiled_hrs: output/review/model/compiled_HR_results_addiction_electively_unvaccinated.csv
        compiled_event_counts: output/review/model/compiled_event_counts_addiction_electively_unvaccinated.csv

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 18:28:24

Config

  • Backend:
    TPP
  • Workspace:
    post-covid-vaccinated
  • Branch:
    main
  • Creator:
    RochelleKnight
  • Force run dependencies:
    False
  • Git Commit Hash:
    a8d8343
  • Requested actions:
    • Analysis_cox_angina_vaccinated