Job request: 14814

Organisation:: University of Bristol
Workspace:: post-covid-diabetes
ID:: tpu3mixa2u7hux5i
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

Action:

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Failed

Job identifier:

nuqo5sl3kgxactar
Action:

stata_cox_model_otherdm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Succeeded

Job identifier:

t6a47ne5n3t6wuda
Action:

stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

5piy6x2zavcq4yow
Action:

stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

63rd2dnaxiatutqb
Action:

stata_cox_model_gestationaldm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Succeeded

Job identifier:

fvq3m4y7x4qz2ysa
Action:

stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Failed

Job identifier:

j7lpehqymydjnays
Action:

stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

zyp7dxef5c65ytbp
Action:

stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Failed

Job identifier:

5dsyd52zmgw43re3
Action:

stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

bzgabjgdaz7gbfzn
Action:

stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

rn6ytibzrllwcz2y
Action:

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Failed

Job identifier:

dgiknrr7zi7fjyfe
Action:

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

5rkochnxerg7gql5
Action:

stata_cox_model_t1dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Succeeded

Job identifier:

p75isgtbympvse4y
Action:

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

ryn3zf3p3luvco5s
Action:

stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

mtklytgq6izc6bdq
Action:

stata_cox_model_t2dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Failed

Job identifier:

4tluy6363eapbyof
Action:

stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

Status:

Status: Failed

Job identifier:

ix72qduxxpyjk4ul
Action:

stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

Status:

Status: Succeeded

Job identifier:

2wjzta5trgxxjpwn
Action:

format_hazard_ratios

Status:

Status: Failed

Job identifier:

5mo77hq47jaatgz5
Action:

format_stata_output

Status:

Status: Failed

Job identifier:

et7bsw243vufxxp3
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
        end_date_table_csv: output/follow_up_end_dates_prevax_*.csv.gz

  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
        end_date_table_csv: output/follow_up_end_dates_vax_*.csv.gz

  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
        end_date_table_csv: output/follow_up_end_dates_unvax_*.csv.gz

  generate_study_population_prevax_diabetes_analyis:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prevax_diabetes_analysis
      --output-format feather
    needs:
    - vax_eligibility_inputs
    - stage1_data_cleaning_prevax
    - stage1_end_date_table_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:
    - vax_eligibility_inputs
    - stage1_data_cleaning_vax
    - stage1_end_date_table_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:
    - vax_eligibility_inputs
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_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
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_prevax.csv
        histograms: output/review/descriptives/days_*_prevax.png
      highly_sensitive:
        cohort_new: output/input_prevax_stage1_diabetes.rds

  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
    - stage1_data_cleaning_vax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_vax.csv
        histograms: output/review/descriptives/days_*_vax.png
      highly_sensitive:
        cohort_new: output/input_vax_stage1_diabetes.rds

  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
    - stage1_data_cleaning_unvax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_*_unvax.csv
        histograms: output/review/descriptives/days_*_unvax.png
      highly_sensitive:
        cohort_new: output/input_unvax_stage1_diabetes.rds

  diabetes_post_hoc_prevax_extended_follow_up:
    run: r:latest analysis/descriptives/diabetes-follow-up-analysis-extended-follow-up.R
      prevax
    needs:
    - generate_study_population_prevax_diabetes_analyis
    - generate_study_population_vax_diabetes_analyis
    - generate_study_population_unvax_diabetes_analyis
    - vax_eligibility_inputs
    - stage1_data_cleaning_prevax
    outputs:
      moderately_sensitive:
        res_table: output/review/descriptives/diabetes_posthoc_analysis_res_EXTENDED_*_prevax.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

  ## Cox model for t1dm - prevax 

  Analysis_cox_t1dm_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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_rec - prevax 

  Analysis_cox_t2dm_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_rec prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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_pre_rec - prevax 

  Analysis_cox_t2dm_pre_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pre_rec prevax TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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_post_rec - prevax 

  Analysis_cox_t2dm_post_rec_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_post_rec prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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

  ## Cox model for t2dm_follow - prevax 

  Analysis_cox_t2dm_follow_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_follow prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_follow_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_follow_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_follow_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_follow_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_follow_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_follow_*_prevax_*_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 TRUE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_vax
    - diabetes_post_hoc_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 FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_unvax
    - diabetes_post_hoc_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 t1dm_extended_follow_up - prevax 

  Analysis_cox_t1dm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t1dm_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t1dm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t1dm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t1dm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t1dm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t1dm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t1dm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t1dm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t1dm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_extended_follow_up - prevax 

  Analysis_cox_t2dm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for otherdm_extended_follow_up - prevax 

  Analysis_cox_otherdm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R otherdm_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_otherdm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_otherdm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_otherdm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_otherdm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_otherdm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_otherdm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_otherdm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_otherdm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for gestationaldm_extended_follow_up - prevax 

  Analysis_cox_gestationaldm_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R gestationaldm_extended_follow_up
      prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_gestationaldm_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_gestationaldm_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_gestationaldm_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_gestationaldm_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_gestationaldm_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_gestationaldm_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_gestationaldm_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_follow_extended_follow_up - prevax 

  Analysis_cox_t2dm_follow_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_follow_extended_follow_up
      prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_follow_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_follow_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_follow_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_follow_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_follow_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd_extended_follow_up - prevax 

  Analysis_cox_t2dm_pd_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_pd_no_extended_follow_up - prevax 

  Analysis_cox_t2dm_pd_no_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_pd_no_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_pd_no_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_pd_no_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_pd_no_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_pd_no_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_pd_no_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes_extended_follow_up - prevax 

  Analysis_cox_t2dm_obes_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_extended_follow_up prevax
      FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_extended_follow_up_*_prevax_*_time_periods.csv

  ## Cox model for t2dm_obes_no_extended_follow_up - prevax 

  Analysis_cox_t2dm_obes_no_extended_follow_up_prevax:
    run: r:latest analysis/model/01_cox_pipeline.R t2dm_obes_no_extended_follow_up
      prevax FALSE
    needs:
    - stage1_data_cleaning_prevax
    - stage1_data_cleaning_vax
    - stage1_data_cleaning_unvax
    - stage1_end_date_table_prevax
    - diabetes_post_hoc_prevax
    outputs:
      moderately_sensitive:
        analyses_not_run: output/review/model/*/analyses_not_run_t2dm_obes_no_extended_follow_up_prevax.csv
        compiled_hrs_csv: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_extended_follow_up_prevax.csv
        compiled_hrs_csv_to_release: output/review/model/*/suppressed_compiled_HR_results_t2dm_obes_no_extended_follow_up_prevax_to_release.csv
        compiled_event_counts_csv: output/review/model/*/suppressed_compiled_event_counts_t2dm_obes_no_extended_follow_up_prevax.csv
        compiled_event_counts_csv_non_supressed: output/review/model/*/compiled_event_counts_t2dm_obes_no_extended_follow_up_prevax.csv
        describe_data_surv: output/not-for-review/describe_data_surv_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.txt
      highly_sensitive:
        dataset: output/input_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.csv
        sampled_dataset: output/input_sampled_data_t2dm_obes_no_extended_follow_up_*_prevax_*_time_periods.csv

  stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_vax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_main_vax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_vax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_main_unvax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_unvax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_follow_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_rec_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_main_prevax_reduced_day0FALSE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods
      FALSE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfFALSE.txt

  stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_t2dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_main_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_t1dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_otherdm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods
      FALSE TRUE
    needs:
    - Analysis_cox_gestationaldm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_stata_median_fup_day0FALSE_extfTRUE.csv
        stata_output: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_reduced_time_periods_cox_model_day0FALSE_extfTRUE.txt

  stata_cox_model_t1dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t1dm_extended_follow_up_main_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_t1dm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_t1dm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_otherdm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_otherdm_extended_follow_up_main_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_otherdm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_otherdm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_gestationaldm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_gestationaldm_extended_follow_up_main_prevax_day_zero_reduced_time_periods
      TRUE TRUE
    needs:
    - Analysis_cox_gestationaldm_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfTRUE.csv
        stata_output: output/input_sampled_data_gestationaldm_extended_follow_up_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfTRUE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_main_vax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_main_unvax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_main_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_vax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_unvax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_follow_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_follow_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_pre_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_pre_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_pre_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  stata_cox_model_t2dm_post_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE:
    run: stata-mp:latest analysis/cox_model.do input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods
      TRUE FALSE
    needs:
    - Analysis_cox_t2dm_post_rec_prevax
    outputs:
      moderately_sensitive:
        medianfup: output/input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods_stata_median_fup_day0TRUE_extfFALSE.csv
        stata_output: output/input_sampled_data_t2dm_post_rec_main_prevax_day_zero_reduced_time_periods_cox_model_day0TRUE_extfFALSE.txt

  format_stata_output:
    run: r:latest analysis/format_stata_output.R
    needs:
    - stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_vax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_main_vax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_main_unvax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_follow_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_rec_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_post_rec_main_prevax_reduced_day0FALSE_extfFALSE
    - stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_t2dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE
    - stata_cox_model_t1dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_otherdm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_gestationaldm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_main_vax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_main_unvax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_vax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_covid_pheno_non_hospitalised_unvax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_follow_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_follow_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_post_rec_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_pre_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    - stata_cox_model_t2dm_post_rec_main_prevax_day_zero_reduced_day0TRUE_extfFALSE
    outputs:
      moderately_sensitive:
        stata_output: output/stata_output.csv

  format_hazard_ratios:
    run: r:latest analysis/model/format_hazard_ratio_outputs.R
    needs:
    - format_stata_output
    - stage4_table_2_prevax
    - stage4_table_2_vax
    - stage4_table_2_unvax
    - Analysis_cox_t1dm_prevax
    - Analysis_cox_t1dm_vax
    - Analysis_cox_t1dm_unvax
    - Analysis_cox_t2dm_prevax
    - Analysis_cox_t2dm_vax
    - Analysis_cox_t2dm_unvax
    - Analysis_cox_t2dm_pre_rec_prevax
    - Analysis_cox_t2dm_pre_rec_vax
    - Analysis_cox_t2dm_pre_rec_unvax
    - Analysis_cox_t2dm_pd_prevax
    - Analysis_cox_t2dm_pd_vax
    - Analysis_cox_t2dm_pd_unvax
    - Analysis_cox_t2dm_pd_no_prevax
    - Analysis_cox_t2dm_pd_no_vax
    - Analysis_cox_t2dm_pd_no_unvax
    - Analysis_cox_t2dm_obes_prevax
    - Analysis_cox_t2dm_obes_vax
    - Analysis_cox_t2dm_obes_unvax
    - Analysis_cox_t2dm_obes_no_prevax
    - Analysis_cox_t2dm_obes_no_vax
    - Analysis_cox_t2dm_obes_no_unvax
    - Analysis_cox_otherdm_prevax
    - Analysis_cox_otherdm_vax
    - Analysis_cox_otherdm_unvax
    - Analysis_cox_gestationaldm_prevax
    - Analysis_cox_gestationaldm_vax
    - Analysis_cox_gestationaldm_unvax
    - Analysis_cox_t2dm_rec_prevax
    - Analysis_cox_t2dm_post_rec_prevax
    - Analysis_cox_t2dm_follow_prevax
    - Analysis_cox_t1dm_extended_follow_up_prevax
    - Analysis_cox_t2dm_extended_follow_up_prevax
    - Analysis_cox_otherdm_extended_follow_up_prevax
    - Analysis_cox_gestationaldm_extended_follow_up_prevax
    - Analysis_cox_t2dm_follow_extended_follow_up_prevax
    - Analysis_cox_t2dm_pd_extended_follow_up_prevax
    - Analysis_cox_t2dm_pd_no_extended_follow_up_prevax
    - Analysis_cox_t2dm_obes_extended_follow_up_prevax
    - Analysis_cox_t2dm_obes_no_extended_follow_up_prevax
    outputs:
      moderately_sensitive:
        hr_output: output/review/model/hr_output_formatted.csv
        hr_output_no_events: output/review/model/hr_output_formatted_no_event_counts.csv
        table2_output: output/review/model/table2_output_formatted_no_hrs.csv
Timeline

Created: 10 months ago 30 Jan 2023 15:01:56 UTC
Started: 10 months ago 30 Jan 2023 15:01:59 UTC
Finished: 10 months ago 30 Jan 2023 16:48:45 UTC
Runtime: 11:11:53
These timestamps are generated and stored using the UTC timezone on the TPP backend.
Job information

Status: Failed
Backend: TPP
Workspace: post-covid-diabetes
Requested by: Kurt Taylor
Branch: main
Force run dependencies: No
Git commit hash: 136697a
Requested actions: stata_cox_model_t2dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_t2dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_t2dm_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_t2dm_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_t2dm_follow_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_non_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_t2dm_follow_extended_follow_up_covid_pheno_hospitalised_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_t1dm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_otherdm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_gestationaldm_extended_follow_up_main_prevax_reduced_day0FALSE_extfTRUE

stata_cox_model_t1dm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_otherdm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

stata_cox_model_gestationaldm_extended_follow_up_main_prevax_day_zero_reduced_day0TRUE_extfTRUE

format_stata_output

format_hazard_ratios