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

  stage_2_events_split_by_covariate_level_vaccinated:
    run: r:latest analysis/descriptives/events_split_by_covariate_level.R vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      moderately_sensitive:
        counts_by_covariate_level: output/not-for-review/event_counts_by_covariate_level_vaccinated_*.csv
        selected_covariates: output/not-for-review/non_zero_selected_covariates_vaccinated_*.csv

  stage_2_events_split_by_covariate_level_electively_unvaccinated:
    run: r:latest analysis/descriptives/events_split_by_covariate_level.R electively_unvaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_electively_unvaccinated
    outputs:
      moderately_sensitive:
        counts_by_covariate_level: output/not-for-review/event_counts_by_covariate_level_electively_unvaccinated_*.csv
        selected_covariates: output/not-for-review/non_zero_selected_covariates_electively_unvaccinated_*.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_*

  reusableaction_input:
    run: r:latest analysis/reusableaction_input.R ami vaccinated
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    outputs:
      highly_sensitive:
        cohort: output/reusableaction_input_*

  reusableaction_model_main:
    run: cox-ipw:v0.0.4 --df_input=reusableaction_input_vaccinated_ami_main_analysis.csv
      --outcome=out_date_ami --covariate_other=cov_num_consulation_rate;cov_bin_healthcare_worker;cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_lipid_medications;cov_bin_antiplatelet_medications;cov_bin_anticoagulation_medications;cov_bin_combined_oral_contraceptive_pill;cov_bin_hormone_replacement_therapy;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease
      --covariate_protect=cov_cat_sex;cov_num_age;cov_cat_region;cov_cat_ethnicity
      --cox_start=index_date --cox_stop=follow_up_end --controls_per_case=20 --df_output=results_vaccinated_ami_main.csv
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - reusableaction_input
    outputs:
      moderately_sensitive:
        arguments: output/args-results_vaccinated_ami_main.csv
        estimates: output/results_vaccinated_ami_main.csv

  reusableaction_model_hospitalised:
    run: cox-ipw:v0.0.4 --df_input=reusableaction_input_vaccinated_ami_hospitalised_analysis.csv
      --outcome=out_date_ami --covariate_other=cov_num_consulation_rate;cov_bin_healthcare_worker;cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_bin_lipid_medications;cov_bin_antiplatelet_medications;cov_bin_anticoagulation_medications;cov_bin_combined_oral_contraceptive_pill;cov_bin_hormone_replacement_therapy;cov_bin_ami;cov_bin_all_stroke;cov_bin_other_arterial_embolism;cov_bin_vte;cov_bin_hf;cov_bin_angina;cov_bin_dementia;cov_bin_liver_disease;cov_bin_chronic_kidney_disease;cov_bin_cancer;cov_bin_hypertension;cov_bin_diabetes;cov_bin_obesity;cov_bin_depression;cov_bin_chronic_obstructive_pulmonary_disease
      --covariate_protect=cov_cat_sex;cov_num_age;cov_cat_region;cov_cat_ethnicity
      --cox_start=index_date --cox_stop=follow_up_end --controls_per_case=20 --df_output=results_vaccinated_ami_hospitalised.csv
    needs:
    - stage1_data_cleaning_both
    - stage1_end_date_table_vaccinated
    - reusableaction_input
    outputs:
      moderately_sensitive:
        arguments: output/args-results_vaccinated_ami_hospitalised.csv
        estimates: output/results_vaccinated_ami_hospitalised.csv

  ## 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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ami_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ami_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ami_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ami_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_isch_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_isch_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_isch_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_isch_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_dvt_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_dvt_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_dvt_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_dvt_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_pe_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_pe_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_pe_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_pe_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_tia_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_tia_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_tia_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_tia_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_stroke_sah_hs_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_stroke_sah_hs_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_hf_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_hf_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_hf_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_hf_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_angina_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_angina_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_angina_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_angina_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_ate_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_ate_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_ate_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_ate_primary_position_*_electively_unvaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_vaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_vaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_vaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_primary_position_*_vaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_primary_position_*_vaccinated_*_time_periods.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
    - stage_2_events_split_by_covariate_level_electively_unvaccinated
    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
        compiled_event_counts_csv_non_supressed: output/review/model/compiled_event_counts_vte_primary_position_electively_unvaccinated.csv
        describe_data_surv: output/not-for-review/describe_data_surv_vte_primary_position_*_electively_unvaccinated_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_vte_primary_position_*_electively_unvaccinated_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_vte_primary_position_*_electively_unvaccinated_*_time_periods.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

  check_episode_covar_pe-ethnicity_region:
    run: r:latest analysis/descriptives/check_episode_covar.R input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv
      ethnicity;region_name pe-ethnicity_region
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        check: output/pe-ethnicity_region.csv

  check_episode_covar_pe-available_covars:
    run: r:latest analysis/descriptives/check_episode_covar.R input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv
      cov_cat_smoking_status;cov_cat_deprivation;region_name;sex;ethnicity pe-available_covars
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        check: output/pe-available_covars.csv

  cumulative_incidence-input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv:
    run: r:latest analysis/descriptives/cumulative_incidence.R input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        cumulative_outcome_plot: output/cumulative-input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.jpeg
        cumulative_outcome_data: output/cumulative-input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv

  cumulative_incidence-input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv:
    run: r:latest analysis/descriptives/cumulative_incidence.R input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv
    needs:
    - Analysis_cox_ate_electively_unvaccinated
    outputs:
      moderately_sensitive:
        cumulative_outcome_plot: output/cumulative-input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.jpeg
        cumulative_outcome_data: output/cumulative-input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv

  region_cumulative_incidence-input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv:
    run: r:latest analysis/descriptives/region_cumulative_incidence.R input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        region_cumulative_outcome_plot: output/region_cumulative-input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.jpeg
        region_cumulative_outcome_data: output/region_cumulative-input_pe_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv

  region_cumulative_incidence-input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv:
    run: r:latest analysis/descriptives/region_cumulative_incidence.R input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv
    needs:
    - Analysis_cox_ate_electively_unvaccinated
    outputs:
      moderately_sensitive:
        region_cumulative_outcome_plot: output/region_cumulative-input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.jpeg
        region_cumulative_outcome_data: output/region_cumulative-input_ate_covid_pheno_hospitalised_electively_unvaccinated_covariate_testing_normal.csv

  stata_model:
    run: stata-mp:latest analysis/cox_model.do
    needs:
    - Analysis_cox_pe_electively_unvaccinated
    outputs:
      moderately_sensitive:
        log_file: output/stata_cox_model.log