Skip to content

Job request: 12514

Organisation:
University of Bristol
Workspace:
diabetes-post-hoc-analysis
ID:
s7lxylhvyde7sqqk
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Kurt Taylor requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 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_prevax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R prevax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_prevax.csv
        QA_rules: output/review/descriptives/QA_summary_prevax_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_prevax_*.csv
        histograms: output/not-for-review/numeric_histograms_prevax_*.svg
      highly_sensitive:
        cohort: output/input_prevax_*.rds
        cohort_csv: output/input_prevax_*.csv.gz

  stage1_data_cleaning_vax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R vax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_vax.csv
        QA_rules: output/review/descriptives/QA_summary_vax_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_vax_*.csv
        histograms: output/not-for-review/numeric_histograms_vax_*.svg
      highly_sensitive:
        cohort: output/input_vax_*.rds
        cohort_csv: output/input_vax_*.csv.gz

  stage1_data_cleaning_unvax:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R unvax
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_unvax.csv
        QA_rules: output/review/descriptives/QA_summary_unvax_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_unvax_*.csv
        histograms: output/not-for-review/numeric_histograms_unvax_*.svg
      highly_sensitive:
        cohort: output/input_unvax_*.rds
        cohort_csv: output/input_unvax_*.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_prevax
    - 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_vax
    - 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_unvax
    - 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_prevax
    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_vax
    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_unvax
    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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - 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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 71:07:19

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
diabetes-post-hoc-analysis
Requested by
Kurt Taylor
Branch
add-new-diabetes-analyses
Force run dependencies
No
Git commit hash
f7544ff
Requested actions
  • stage1_data_cleaning_prevax
  • stage1_data_cleaning_vax
  • stage1_data_cleaning_unvax
  • stage1_end_date_table_prevax
  • stage1_end_date_table_vax
  • stage1_end_date_table_unvax
  • generate_study_population_prevax_diabetes_analyis
  • generate_study_population_vax_diabetes_analyis
  • generate_study_population_unvax_diabetes_analyis
  • diabetes_post_hoc_prevax
  • diabetes_post_hoc_vax
  • diabetes_post_hoc_unvax
  • stage2_missing_table1_all
  • stage3_diabetes_flow_prevax
  • stage3_diabetes_flow_vax
  • stage3_diabetes_flow_unvax
  • stage4_table_2_prevax
  • stage4_table_2_vax
  • stage4_table_2_unvax
  • stage4_venn_diagram_all