project.yaml

version: '3.0'

expectations:

  population_size: 200000

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/metadates.R
    outputs:
      highly_sensitive:
        study_dates_json: output/study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_prelim:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_prelim.feather

  generate_index_dates:
    run: r:latest analysis/prelim.R
    needs:
    - vax_eligibility_inputs
    - generate_study_population_prelim
    outputs:
      highly_sensitive:
        index_dates: output/index_dates.csv

  generate_study_population_prevax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_prevax.feather

  generate_study_population_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format feather
    needs:
    - generate_index_dates
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather

  generate_study_population_unvax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_unvax.feather

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prelim
    - generate_study_population_prevax
    - generate_study_population_vax
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_*.txt
      highly_sensitive:
        cohort: output/input_prevax.rds
        venn: output/venn_prevax.rds

  preprocess_data_vax:
    run: r:latest analysis/preprocess/preprocess_data.R vax
    needs:
    - generate_index_dates
    - generate_study_population_prelim
    - generate_study_population_prevax
    - generate_study_population_vax
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_*.txt
      highly_sensitive:
        cohort: output/input_vax.rds
        venn: output/venn_vax.rds

  preprocess_data_unvax:
    run: r:latest analysis/preprocess/preprocess_data.R unvax
    needs:
    - generate_index_dates
    - generate_study_population_prelim
    - generate_study_population_prevax
    - generate_study_population_vax
    - generate_study_population_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_*.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

  stage1_data_cleaning_all:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R all
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    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_*.rds
        cohort_csv: output/input_*.csv.gz

  stage1_end_date_table_prevax:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R prevax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - stage1_data_cleaning_all
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_prevax_*.rds

  stage1_end_date_table_vax:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R vax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - stage1_data_cleaning_all
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_vax_*.rds

  stage1_end_date_table_unvax:
    run: r:latest analysis/preprocess/create_follow_up_end_date.R unvax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - stage1_data_cleaning_all
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        end_date_table: output/follow_up_end_dates_unvax_*.rds

  generate_study_population_prevax_diabetes_analyis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_diabetes_analysis
      --output-format feather
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        cohort: output/input_prevax_diabetes_analysis.feather

  generate_study_population_vax_diabetes_analyis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax_diabetes_analysis
      --output-format feather
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        cohort: output/input_vax_diabetes_analysis.feather

  generate_study_population_unvax_diabetes_analyis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_unvax_diabetes_analysis
      --output-format feather
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        cohort: output/input_unvax_diabetes_analysis.feather

  diabetes_post_hoc_prevax:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R prevax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_prevax.csv

  diabetes_post_hoc_vax:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R vax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_vax.csv

  diabetes_post_hoc_unvax:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis.R unvax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_unvax.csv

  stage2_missing_table1_all:
    run: r:latest analysis/descriptives/Stage2_missing_table1.R all
    needs:
    - stage1_data_cleaning_all
    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_prevax:
    run: r:latest analysis/descriptives/diabetes_flowchart.R prevax
    needs:
    - stage1_data_cleaning_all
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_prevax_*.csv

  stage3_diabetes_flow_vax:
    run: r:latest analysis/descriptives/diabetes_flowchart.R vax
    needs:
    - stage1_data_cleaning_all
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_vax_*.csv

  stage3_diabetes_flow_unvax:
    run: r:latest analysis/descriptives/diabetes_flowchart.R unvax
    needs:
    - stage1_data_cleaning_all
    outputs:
      moderately_sensitive:
        flow_df: output/review/figure-data/diabetes_flow_values_unvax_*.csv

  ## Stage 4 - Table 2 - prevax cohort 

  stage4_table_2_prevax:
    run: r:latest analysis/descriptives/table_2.R prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_prevax_*.csv

  ## Stage 4 - Table 2 - vax cohort 

  stage4_table_2_vax:
    run: r:latest analysis/descriptives/table_2.R vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_vax_*.csv

  ## Stage 4 - Table 2 - unvax cohort 

  stage4_table_2_unvax:
    run: r:latest analysis/descriptives/table_2.R unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_unvax_*.csv

  stage4_venn_diagram_all:
    run: r:latest analysis/descriptives/venn_diagram.R all
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    - stage1_end_date_table_vax
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_*

  ## Cox model for t1dm - prevax 

  Analysis_cox_t1dm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_*_prevax_*_time_periods.csv

  ## Cox model for t1dm - vax 

  Analysis_cox_t1dm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_*_vax_*_time_periods.csv

  ## Cox model for t1dm - unvax 

  Analysis_cox_t1dm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_*_unvax_*_time_periods.csv

  ## Cox model for t2dm - prevax 

  Analysis_cox_t2dm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_*_prevax_*_time_periods.csv

  ## Cox model for t2dm - vax 

  Analysis_cox_t2dm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_*_vax_*_time_periods.csv

  ## Cox model for t2dm - unvax 

  Analysis_cox_t2dm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_pre_rec - prevax 

  Analysis_cox_t2dm_pre_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pre_rec_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pre_rec - vax 

  Analysis_cox_t2dm_pre_rec_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pre_rec_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_vax_*_time_periods.csv

  ## Cox model for t2dm_pre_rec - unvax 

  Analysis_cox_t2dm_pre_rec_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pre_rec_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pre_rec_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pre_rec_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pre_rec_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pre_rec_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pre_rec_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pre_rec_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_pd - prevax 

  Analysis_cox_t2dm_pd_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd - vax 

  Analysis_cox_t2dm_pd_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_*_vax_*_time_periods.csv

  ## Cox model for t2dm_pd - unvax 

  Analysis_cox_t2dm_pd_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_pd_no - prevax 

  Analysis_cox_t2dm_pd_no_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd_no - vax 

  Analysis_cox_t2dm_pd_no_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_vax_*_time_periods.csv

  ## Cox model for t2dm_pd_no - unvax 

  Analysis_cox_t2dm_pd_no_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_obes - prevax 

  Analysis_cox_t2dm_obes_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes - vax 

  Analysis_cox_t2dm_obes_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_*_vax_*_time_periods.csv

  ## Cox model for t2dm_obes - unvax 

  Analysis_cox_t2dm_obes_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_obes_no - prevax 

  Analysis_cox_t2dm_obes_no_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes_no - vax 

  Analysis_cox_t2dm_obes_no_vax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_vax_*_time_periods.csv

  ## Cox model for t2dm_obes_no - unvax 

  Analysis_cox_t2dm_obes_no_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_*_unvax_*_time_periods.csv

  ## Cox model for otherdm - prevax 

  Analysis_cox_otherdm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_*_prevax_*_time_periods.csv

  ## Cox model for otherdm - vax 

  Analysis_cox_otherdm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_*_vax_*_time_periods.csv

  ## Cox model for otherdm - unvax 

  Analysis_cox_otherdm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_*_unvax_*_time_periods.csv

  ## Cox model for gestationaldm - prevax 

  Analysis_cox_gestationaldm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_*_prevax_*_time_periods.csv

  ## Cox model for gestationaldm - vax 

  Analysis_cox_gestationaldm_vax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm vax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_vax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_vax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_vax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_vax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_vax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_vax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_vax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_*_vax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_*_vax_*_time_periods.csv

  ## Cox model for gestationaldm - unvax 

  Analysis_cox_gestationaldm_unvax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm unvax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_unvax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_unvax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_unvax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_unvax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_unvax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_*_unvax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_*_unvax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_*_unvax_*_time_periods.csv

  ## Cox model for t2dm_rec - prevax 

  Analysis_cox_t2dm_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_rec prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_rec_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_rec_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_rec_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_rec_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_rec_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_rec_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_rec_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_rec_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_post_rec - prevax 

  Analysis_cox_t2dm_post_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_post_rec prevax
    needs:
    - stage1_data_cleaning_all
    - stage1_end_date_table_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_post_rec_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_post_rec_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_post_rec_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_post_rec_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_post_rec_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_post_rec_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_post_rec_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_post_rec_*_prevax_*_time_periods.csv