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Job request: 14702

Workspace:
gastrointestinal_cox
ID:
spal4ttcxeowyyi3

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

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

Jobs

Pipeline

Show project.yaml
version: '3.0'

expectations:

  population_size: 10000

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 csv.gz
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_prelim.csv.gz

  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.gz

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

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

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

  preprocess_data_prevax:
    run: r:latest analysis/preprocess/preprocess_data.R prevax
    needs:
    - generate_index_dates
    - generate_study_population_prevax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_prevax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_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_vax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_vax_stage0.txt
        descrive_venn: output/not-for-review/describe_venn_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_unvax
    outputs:
      moderately_sensitive:
        describe: output/not-for-review/describe_input_unvax_stage0.txt
        describe_venn: output/not-for-review/describe_venn_unvax.txt
      highly_sensitive:
        cohort: output/input_unvax.rds
        venn: output/venn_unvax.rds

  stage1_data_cleaning_all:
    run: r:latest analysis/preprocess/Stage1_data_cleaning.R all
    needs:
    - preprocess_data_prevax
    - preprocess_data_vax
    - preprocess_data_unvax
    - vax_eligibility_inputs
    outputs:
      moderately_sensitive:
        refactoring: output/not-for-review/meta_data_factors_*.csv
        QA_rules: output/review/descriptives/QA_summary_*.csv
        IE_criteria: output/review/descriptives/Cohort_flow_*.csv
        histograms: output/not-for-review/numeric_histograms_*.svg
      highly_sensitive:
        cohort: output/input_*.rds

  stage2_missing_table1_all:
    run: r:latest analysis/descriptives/Stage2_missing_table1.R all
    needs:
    - stage1_data_cleaning_all
    outputs:
      moderately_sensitive:
        Missing_RangeChecks: output/not-for-review/Check_missing_range_*.csv
        DateChecks: output/not-for-review/Check_dates_range_*.csv
        Descriptive_Table: output/review/descriptives/Table1_*.csv

  ## Stage 3 - Table 2 - prevax cohort 

  stage3_table_2_prevax:
    run: r:latest analysis/descriptives/table_2.R prevax
    needs:
    - stage1_data_cleaning_all
    - make_model_input-cohort_prevax-main-abdominal_distension
    - make_model_input-cohort_prevax-main-abdominal_paindiscomfort
    - make_model_input-cohort_prevax-main-acute_pancreatitis
    - make_model_input-cohort_prevax-main-appendicitis
    - make_model_input-cohort_prevax-main-belching
    - make_model_input-cohort_prevax-main-bloody_stools
    - make_model_input-cohort_prevax-main-bowel_ischaemia
    - make_model_input-cohort_prevax-main-diarrhoea
    - make_model_input-cohort_prevax-main-dyspepsia
    - make_model_input-cohort_prevax-main-gallstones_disease
    - make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
    - make_model_input-cohort_prevax-main-ibs
    - make_model_input-cohort_prevax-main-intestinal_obstruction
    - make_model_input-cohort_prevax-main-lower_gi_bleeding
    - make_model_input-cohort_prevax-main-nausea
    - make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
    - make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
    - make_model_input-cohort_prevax-main-peptic_ulcer
    - make_model_input-cohort_prevax-main-upper_gi_bleeding
    - make_model_input-cohort_prevax-main-variceal_gi_bleeding
    - make_model_input-cohort_prevax-main-vomiting
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_prevax.csv

  ## Stage 3 - Table 2 - unvax cohort 

  stage3_table_2_unvax:
    run: r:latest analysis/descriptives/table_2.R unvax
    needs:
    - stage1_data_cleaning_all
    - make_model_input-cohort_unvax-main-abdominal_distension
    - make_model_input-cohort_unvax-main-abdominal_paindiscomfort
    - make_model_input-cohort_unvax-main-acute_pancreatitis
    - make_model_input-cohort_unvax-main-appendicitis
    - make_model_input-cohort_unvax-main-belching
    - make_model_input-cohort_unvax-main-bloody_stools
    - make_model_input-cohort_unvax-main-bowel_ischaemia
    - make_model_input-cohort_unvax-main-diarrhoea
    - make_model_input-cohort_unvax-main-dyspepsia
    - make_model_input-cohort_unvax-main-gallstones_disease
    - make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
    - make_model_input-cohort_unvax-main-ibs
    - make_model_input-cohort_unvax-main-intestinal_obstruction
    - make_model_input-cohort_unvax-main-lower_gi_bleeding
    - make_model_input-cohort_unvax-main-nausea
    - make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
    - make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding
    - make_model_input-cohort_unvax-main-peptic_ulcer
    - make_model_input-cohort_unvax-main-upper_gi_bleeding
    - make_model_input-cohort_unvax-main-variceal_gi_bleeding
    - make_model_input-cohort_unvax-main-vomiting
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_unvax.csv

  ## Stage 3 - Table 2 - vax cohort 

  stage3_table_2_vax:
    run: r:latest analysis/descriptives/table_2.R vax
    needs:
    - stage1_data_cleaning_all
    - make_model_input-cohort_vax-main-abdominal_distension
    - make_model_input-cohort_vax-main-abdominal_paindiscomfort
    - make_model_input-cohort_vax-main-acute_pancreatitis
    - make_model_input-cohort_vax-main-appendicitis
    - make_model_input-cohort_vax-main-belching
    - make_model_input-cohort_vax-main-bloody_stools
    - make_model_input-cohort_vax-main-bowel_ischaemia
    - make_model_input-cohort_vax-main-diarrhoea
    - make_model_input-cohort_vax-main-dyspepsia
    - make_model_input-cohort_vax-main-gallstones_disease
    - make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
    - make_model_input-cohort_vax-main-ibs
    - make_model_input-cohort_vax-main-intestinal_obstruction
    - make_model_input-cohort_vax-main-lower_gi_bleeding
    - make_model_input-cohort_vax-main-nausea
    - make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis
    - make_model_input-cohort_vax-main-nonvariceal_gi_bleeding
    - make_model_input-cohort_vax-main-peptic_ulcer
    - make_model_input-cohort_vax-main-upper_gi_bleeding
    - make_model_input-cohort_vax-main-variceal_gi_bleeding
    - make_model_input-cohort_vax-main-vomiting
    outputs:
      moderately_sensitive:
        input_table_2: output/review/descriptives/table2_vax.csv

  ## Stage 4a - Venn diagrams prevax 

  stage4_venn_diagram_prevax:
    run: r:latest analysis/descriptives/venn_diagram.R prevax
    needs:
    - preprocess_data_prevax
    - make_model_input-cohort_prevax-main-abdominal_distension
    - make_model_input-cohort_prevax-main-abdominal_paindiscomfort
    - make_model_input-cohort_prevax-main-acute_pancreatitis
    - make_model_input-cohort_prevax-main-appendicitis
    - make_model_input-cohort_prevax-main-belching
    - make_model_input-cohort_prevax-main-bloody_stools
    - make_model_input-cohort_prevax-main-bowel_ischaemia
    - make_model_input-cohort_prevax-main-diarrhoea
    - make_model_input-cohort_prevax-main-dyspepsia
    - make_model_input-cohort_prevax-main-gallstones_disease
    - make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
    - make_model_input-cohort_prevax-main-ibs
    - make_model_input-cohort_prevax-main-intestinal_obstruction
    - make_model_input-cohort_prevax-main-lower_gi_bleeding
    - make_model_input-cohort_prevax-main-nausea
    - make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
    - make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
    - make_model_input-cohort_prevax-main-peptic_ulcer
    - make_model_input-cohort_prevax-main-upper_gi_bleeding
    - make_model_input-cohort_prevax-main-variceal_gi_bleeding
    - make_model_input-cohort_prevax-main-vomiting
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_number_check_prevax.csv

  ## Stage 4b - Venn diagrams vax 

  stage4_venn_diagram_vax:
    run: r:latest analysis/descriptives/venn_diagram.R vax
    needs:
    - preprocess_data_vax
    - make_model_input-cohort_vax-main-abdominal_distension
    - make_model_input-cohort_vax-main-abdominal_paindiscomfort
    - make_model_input-cohort_vax-main-acute_pancreatitis
    - make_model_input-cohort_vax-main-appendicitis
    - make_model_input-cohort_vax-main-belching
    - make_model_input-cohort_vax-main-bloody_stools
    - make_model_input-cohort_vax-main-bowel_ischaemia
    - make_model_input-cohort_vax-main-diarrhoea
    - make_model_input-cohort_vax-main-dyspepsia
    - make_model_input-cohort_vax-main-gallstones_disease
    - make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
    - make_model_input-cohort_vax-main-ibs
    - make_model_input-cohort_vax-main-intestinal_obstruction
    - make_model_input-cohort_vax-main-lower_gi_bleeding
    - make_model_input-cohort_vax-main-nausea
    - make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis
    - make_model_input-cohort_vax-main-nonvariceal_gi_bleeding
    - make_model_input-cohort_vax-main-peptic_ulcer
    - make_model_input-cohort_vax-main-upper_gi_bleeding
    - make_model_input-cohort_vax-main-variceal_gi_bleeding
    - make_model_input-cohort_vax-main-vomiting
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_number_check_vax.csv

  ## Stage 4c - Venn diagrams unvax 

  stage4_venn_diagram_unvax:
    run: r:latest analysis/descriptives/venn_diagram.R unvax
    needs:
    - preprocess_data_unvax
    - make_model_input-cohort_unvax-main-abdominal_distension
    - make_model_input-cohort_unvax-main-abdominal_paindiscomfort
    - make_model_input-cohort_unvax-main-acute_pancreatitis
    - make_model_input-cohort_unvax-main-appendicitis
    - make_model_input-cohort_unvax-main-belching
    - make_model_input-cohort_unvax-main-bloody_stools
    - make_model_input-cohort_unvax-main-bowel_ischaemia
    - make_model_input-cohort_unvax-main-diarrhoea
    - make_model_input-cohort_unvax-main-dyspepsia
    - make_model_input-cohort_unvax-main-gallstones_disease
    - make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
    - make_model_input-cohort_unvax-main-ibs
    - make_model_input-cohort_unvax-main-intestinal_obstruction
    - make_model_input-cohort_unvax-main-lower_gi_bleeding
    - make_model_input-cohort_unvax-main-nausea
    - make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
    - make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding
    - make_model_input-cohort_unvax-main-peptic_ulcer
    - make_model_input-cohort_unvax-main-upper_gi_bleeding
    - make_model_input-cohort_unvax-main-variceal_gi_bleeding
    - make_model_input-cohort_unvax-main-vomiting
    outputs:
      moderately_sensitive:
        venn_diagram: output/review/venn-diagrams/venn_diagram_number_check_unvax.csv

  ## Stage 5 - Run models 

  make_model_input-cohort_prevax-main-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-abdominal_distension.rds

  describe_model_input-cohort_prevax-main-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_prevax-main-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-abdominal_distension.txt

  cox_ipw-cohort_prevax-main-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-abdominal_distension.csv
    needs:
    - make_model_input-cohort_prevax-main-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-abdominal_distension.csv

  make_model_input-cohort_prevax-main-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-abdominal_paindiscomfort.rds

  describe_model_input-cohort_prevax-main-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_prevax-main-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-abdominal_paindiscomfort.txt

  cox_ipw-cohort_prevax-main-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_prevax-main-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-abdominal_paindiscomfort.csv

  make_model_input-cohort_prevax-main-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-acute_pancreatitis.rds

  describe_model_input-cohort_prevax-main-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_prevax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-acute_pancreatitis.txt

  cox_ipw-cohort_prevax-main-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_prevax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-acute_pancreatitis.csv

  make_model_input-cohort_prevax-main-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-appendicitis.rds

  describe_model_input-cohort_prevax-main-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-appendicitis
      rds
    needs:
    - make_model_input-cohort_prevax-main-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-appendicitis.txt

  cox_ipw-cohort_prevax-main-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-appendicitis.csv
    needs:
    - make_model_input-cohort_prevax-main-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-appendicitis.csv

  make_model_input-cohort_prevax-main-belching:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-belching.rds

  describe_model_input-cohort_prevax-main-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-belching
      rds
    needs:
    - make_model_input-cohort_prevax-main-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-belching.txt

  cox_ipw-cohort_prevax-main-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-belching.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-belching.csv
    needs:
    - make_model_input-cohort_prevax-main-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-belching.csv

  make_model_input-cohort_prevax-main-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-bloody_stools.rds

  describe_model_input-cohort_prevax-main-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-bloody_stools
      rds
    needs:
    - make_model_input-cohort_prevax-main-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-bloody_stools.txt

  cox_ipw-cohort_prevax-main-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-bloody_stools.csv
    needs:
    - make_model_input-cohort_prevax-main-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-bloody_stools.csv

  make_model_input-cohort_prevax-main-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-bowel_ischaemia.rds

  describe_model_input-cohort_prevax-main-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_prevax-main-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-bowel_ischaemia.txt

  cox_ipw-cohort_prevax-main-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_prevax-main-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-bowel_ischaemia.csv

  make_model_input-cohort_prevax-main-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-diarrhoea.rds

  describe_model_input-cohort_prevax-main-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-diarrhoea
      rds
    needs:
    - make_model_input-cohort_prevax-main-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-diarrhoea.txt

  cox_ipw-cohort_prevax-main-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-diarrhoea.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-diarrhoea.csv
    needs:
    - make_model_input-cohort_prevax-main-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-diarrhoea.csv

  make_model_input-cohort_prevax-main-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-dyspepsia.rds

  describe_model_input-cohort_prevax-main-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-dyspepsia
      rds
    needs:
    - make_model_input-cohort_prevax-main-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-dyspepsia.txt

  cox_ipw-cohort_prevax-main-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-dyspepsia.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-dyspepsia.csv
    needs:
    - make_model_input-cohort_prevax-main-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-dyspepsia.csv

  make_model_input-cohort_prevax-main-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-gallstones_disease.rds

  describe_model_input-cohort_prevax-main-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_prevax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-gallstones_disease.txt

  cox_ipw-cohort_prevax-main-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-gallstones_disease.csv
    needs:
    - make_model_input-cohort_prevax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-gallstones_disease.csv

  make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_prevax-main-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_prevax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_prevax-main-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-ibs.rds

  describe_model_input-cohort_prevax-main-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-ibs rds
    needs:
    - make_model_input-cohort_prevax-main-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-ibs.txt

  cox_ipw-cohort_prevax-main-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-ibs.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-ibs.csv
    needs:
    - make_model_input-cohort_prevax-main-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-ibs.csv

  make_model_input-cohort_prevax-main-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-intestinal_obstruction.rds

  describe_model_input-cohort_prevax-main-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_prevax-main-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-intestinal_obstruction.txt

  cox_ipw-cohort_prevax-main-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_prevax-main-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-intestinal_obstruction.csv

  make_model_input-cohort_prevax-main-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-lower_gi_bleeding.rds

  describe_model_input-cohort_prevax-main-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-lower_gi_bleeding.txt

  cox_ipw-cohort_prevax-main-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-lower_gi_bleeding.csv

  make_model_input-cohort_prevax-main-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-nausea.rds

  describe_model_input-cohort_prevax-main-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-nausea rds
    needs:
    - make_model_input-cohort_prevax-main-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-nausea.txt

  cox_ipw-cohort_prevax-main-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nausea.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-nausea.csv
    needs:
    - make_model_input-cohort_prevax-main-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-nausea.csv

  make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_prevax-main-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_prevax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_prevax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_prevax-main-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_prevax-main-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-peptic_ulcer.rds

  describe_model_input-cohort_prevax-main-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_prevax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-peptic_ulcer.txt

  cox_ipw-cohort_prevax-main-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_prevax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-peptic_ulcer.csv

  make_model_input-cohort_prevax-main-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-upper_gi_bleeding.rds

  describe_model_input-cohort_prevax-main-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-upper_gi_bleeding.txt

  cox_ipw-cohort_prevax-main-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-upper_gi_bleeding.csv

  make_model_input-cohort_prevax-main-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-variceal_gi_bleeding.rds

  describe_model_input-cohort_prevax-main-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-variceal_gi_bleeding.txt

  cox_ipw-cohort_prevax-main-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-variceal_gi_bleeding.csv

  make_model_input-cohort_prevax-main-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-main-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-main-vomiting.rds

  describe_model_input-cohort_prevax-main-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-main-vomiting
      rds
    needs:
    - make_model_input-cohort_prevax-main-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-main-vomiting.txt

  cox_ipw-cohort_prevax-main-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-main-vomiting.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-main-vomiting.csv
    needs:
    - make_model_input-cohort_prevax-main-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-main-vomiting.csv

  make_model_input-cohort_unvax-main-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-abdominal_distension.rds

  describe_model_input-cohort_unvax-main-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_unvax-main-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-abdominal_distension.txt

  cox_ipw-cohort_unvax-main-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-abdominal_distension.csv
    needs:
    - make_model_input-cohort_unvax-main-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-abdominal_distension.csv

  make_model_input-cohort_unvax-main-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-abdominal_paindiscomfort.rds

  describe_model_input-cohort_unvax-main-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_unvax-main-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-abdominal_paindiscomfort.txt

  cox_ipw-cohort_unvax-main-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_unvax-main-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-abdominal_paindiscomfort.csv

  make_model_input-cohort_unvax-main-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-acute_pancreatitis.rds

  describe_model_input-cohort_unvax-main-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_unvax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-acute_pancreatitis.txt

  cox_ipw-cohort_unvax-main-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_unvax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-acute_pancreatitis.csv

  make_model_input-cohort_unvax-main-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-appendicitis.rds

  describe_model_input-cohort_unvax-main-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-appendicitis
      rds
    needs:
    - make_model_input-cohort_unvax-main-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-appendicitis.txt

  cox_ipw-cohort_unvax-main-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-appendicitis.csv
    needs:
    - make_model_input-cohort_unvax-main-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-appendicitis.csv

  make_model_input-cohort_unvax-main-belching:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-belching.rds

  describe_model_input-cohort_unvax-main-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-belching
      rds
    needs:
    - make_model_input-cohort_unvax-main-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-belching.txt

  cox_ipw-cohort_unvax-main-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-belching.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-belching.csv
    needs:
    - make_model_input-cohort_unvax-main-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-belching.csv

  make_model_input-cohort_unvax-main-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-bloody_stools.rds

  describe_model_input-cohort_unvax-main-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-bloody_stools
      rds
    needs:
    - make_model_input-cohort_unvax-main-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-bloody_stools.txt

  cox_ipw-cohort_unvax-main-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-bloody_stools.csv
    needs:
    - make_model_input-cohort_unvax-main-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-bloody_stools.csv

  make_model_input-cohort_unvax-main-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-bowel_ischaemia.rds

  describe_model_input-cohort_unvax-main-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_unvax-main-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-bowel_ischaemia.txt

  cox_ipw-cohort_unvax-main-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_unvax-main-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-bowel_ischaemia.csv

  make_model_input-cohort_unvax-main-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-diarrhoea.rds

  describe_model_input-cohort_unvax-main-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-diarrhoea
      rds
    needs:
    - make_model_input-cohort_unvax-main-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-diarrhoea.txt

  cox_ipw-cohort_unvax-main-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-diarrhoea.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-diarrhoea.csv
    needs:
    - make_model_input-cohort_unvax-main-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-diarrhoea.csv

  make_model_input-cohort_unvax-main-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-dyspepsia.rds

  describe_model_input-cohort_unvax-main-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-dyspepsia
      rds
    needs:
    - make_model_input-cohort_unvax-main-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-dyspepsia.txt

  cox_ipw-cohort_unvax-main-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-dyspepsia.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-dyspepsia.csv
    needs:
    - make_model_input-cohort_unvax-main-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-dyspepsia.csv

  make_model_input-cohort_unvax-main-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-gallstones_disease.rds

  describe_model_input-cohort_unvax-main-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_unvax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-gallstones_disease.txt

  cox_ipw-cohort_unvax-main-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-gallstones_disease.csv
    needs:
    - make_model_input-cohort_unvax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-gallstones_disease.csv

  make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_unvax-main-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_unvax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_unvax-main-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-ibs.rds

  describe_model_input-cohort_unvax-main-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-ibs rds
    needs:
    - make_model_input-cohort_unvax-main-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-ibs.txt

  cox_ipw-cohort_unvax-main-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-ibs.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-ibs.csv
    needs:
    - make_model_input-cohort_unvax-main-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-ibs.csv

  make_model_input-cohort_unvax-main-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-intestinal_obstruction.rds

  describe_model_input-cohort_unvax-main-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_unvax-main-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-intestinal_obstruction.txt

  cox_ipw-cohort_unvax-main-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_unvax-main-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-intestinal_obstruction.csv

  make_model_input-cohort_unvax-main-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-lower_gi_bleeding.rds

  describe_model_input-cohort_unvax-main-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-lower_gi_bleeding.txt

  cox_ipw-cohort_unvax-main-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-lower_gi_bleeding.csv

  make_model_input-cohort_unvax-main-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-nausea.rds

  describe_model_input-cohort_unvax-main-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-nausea rds
    needs:
    - make_model_input-cohort_unvax-main-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-nausea.txt

  cox_ipw-cohort_unvax-main-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-nausea.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-nausea.csv
    needs:
    - make_model_input-cohort_unvax-main-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-nausea.csv

  make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_unvax-main-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_unvax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_unvax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_unvax-main-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_unvax-main-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-peptic_ulcer.rds

  describe_model_input-cohort_unvax-main-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_unvax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-peptic_ulcer.txt

  cox_ipw-cohort_unvax-main-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_unvax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-peptic_ulcer.csv

  make_model_input-cohort_unvax-main-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-upper_gi_bleeding.rds

  describe_model_input-cohort_unvax-main-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-upper_gi_bleeding.txt

  cox_ipw-cohort_unvax-main-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-upper_gi_bleeding.csv

  make_model_input-cohort_unvax-main-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-variceal_gi_bleeding.rds

  describe_model_input-cohort_unvax-main-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-variceal_gi_bleeding.txt

  cox_ipw-cohort_unvax-main-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-variceal_gi_bleeding.csv

  make_model_input-cohort_unvax-main-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-main-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-main-vomiting.rds

  describe_model_input-cohort_unvax-main-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-main-vomiting
      rds
    needs:
    - make_model_input-cohort_unvax-main-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-main-vomiting.txt

  cox_ipw-cohort_unvax-main-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-main-vomiting.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-main-vomiting.csv
    needs:
    - make_model_input-cohort_unvax-main-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-main-vomiting.csv

  make_model_input-cohort_vax-main-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-abdominal_distension.rds

  describe_model_input-cohort_vax-main-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_vax-main-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-abdominal_distension.txt

  cox_ipw-cohort_vax-main-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-abdominal_distension.csv
    needs:
    - make_model_input-cohort_vax-main-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-abdominal_distension.csv

  make_model_input-cohort_vax-main-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-abdominal_paindiscomfort.rds

  describe_model_input-cohort_vax-main-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_vax-main-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-abdominal_paindiscomfort.txt

  cox_ipw-cohort_vax-main-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_vax-main-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-abdominal_paindiscomfort.csv

  make_model_input-cohort_vax-main-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-acute_pancreatitis.rds

  describe_model_input-cohort_vax-main-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_vax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-acute_pancreatitis.txt

  cox_ipw-cohort_vax-main-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_vax-main-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-acute_pancreatitis.csv

  make_model_input-cohort_vax-main-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-appendicitis.rds

  describe_model_input-cohort_vax-main-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-appendicitis
      rds
    needs:
    - make_model_input-cohort_vax-main-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-appendicitis.txt

  cox_ipw-cohort_vax-main-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-appendicitis.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-appendicitis.csv
    needs:
    - make_model_input-cohort_vax-main-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-appendicitis.csv

  make_model_input-cohort_vax-main-belching:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-belching.rds

  describe_model_input-cohort_vax-main-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-belching rds
    needs:
    - make_model_input-cohort_vax-main-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-belching.txt

  cox_ipw-cohort_vax-main-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-belching.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-belching.csv
    needs:
    - make_model_input-cohort_vax-main-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-belching.csv

  make_model_input-cohort_vax-main-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-bloody_stools.rds

  describe_model_input-cohort_vax-main-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-bloody_stools
      rds
    needs:
    - make_model_input-cohort_vax-main-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-bloody_stools.txt

  cox_ipw-cohort_vax-main-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-bloody_stools.csv
    needs:
    - make_model_input-cohort_vax-main-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-bloody_stools.csv

  make_model_input-cohort_vax-main-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-bowel_ischaemia.rds

  describe_model_input-cohort_vax-main-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_vax-main-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-bowel_ischaemia.txt

  cox_ipw-cohort_vax-main-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_vax-main-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-bowel_ischaemia.csv

  make_model_input-cohort_vax-main-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-diarrhoea.rds

  describe_model_input-cohort_vax-main-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-diarrhoea rds
    needs:
    - make_model_input-cohort_vax-main-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-diarrhoea.txt

  cox_ipw-cohort_vax-main-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-diarrhoea.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-diarrhoea.csv
    needs:
    - make_model_input-cohort_vax-main-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-diarrhoea.csv

  make_model_input-cohort_vax-main-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-dyspepsia.rds

  describe_model_input-cohort_vax-main-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-dyspepsia rds
    needs:
    - make_model_input-cohort_vax-main-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-dyspepsia.txt

  cox_ipw-cohort_vax-main-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-dyspepsia.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-dyspepsia.csv
    needs:
    - make_model_input-cohort_vax-main-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-dyspepsia.csv

  make_model_input-cohort_vax-main-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-gallstones_disease.rds

  describe_model_input-cohort_vax-main-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_vax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-gallstones_disease.txt

  cox_ipw-cohort_vax-main-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-gallstones_disease.csv
    needs:
    - make_model_input-cohort_vax-main-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-gallstones_disease.csv

  make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_vax-main-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_vax-main-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_vax-main-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-ibs.rds

  describe_model_input-cohort_vax-main-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-ibs rds
    needs:
    - make_model_input-cohort_vax-main-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-ibs.txt

  cox_ipw-cohort_vax-main-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-ibs.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-ibs.csv
    needs:
    - make_model_input-cohort_vax-main-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-ibs.csv

  make_model_input-cohort_vax-main-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-intestinal_obstruction.rds

  describe_model_input-cohort_vax-main-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_vax-main-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-intestinal_obstruction.txt

  cox_ipw-cohort_vax-main-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_vax-main-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-intestinal_obstruction.csv

  make_model_input-cohort_vax-main-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-lower_gi_bleeding.rds

  describe_model_input-cohort_vax-main-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-lower_gi_bleeding.txt

  cox_ipw-cohort_vax-main-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-lower_gi_bleeding.csv

  make_model_input-cohort_vax-main-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-nausea.rds

  describe_model_input-cohort_vax-main-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-nausea rds
    needs:
    - make_model_input-cohort_vax-main-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-nausea.txt

  cox_ipw-cohort_vax-main-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-nausea.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-nausea.csv
    needs:
    - make_model_input-cohort_vax-main-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-nausea.csv

  make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_vax-main-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_vax-main-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;cov_bin_hypertriglyceridemia;cov_bin_hypercalcemia;cov_num_systolic_bp;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_vax-main-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_vax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_vax-main-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_vax-main-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_vax-main-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-peptic_ulcer.rds

  describe_model_input-cohort_vax-main-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_vax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-peptic_ulcer.txt

  cox_ipw-cohort_vax-main-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-peptic_ulcer.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_vax-main-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-peptic_ulcer.csv

  make_model_input-cohort_vax-main-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-upper_gi_bleeding.rds

  describe_model_input-cohort_vax-main-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-upper_gi_bleeding.txt

  cox_ipw-cohort_vax-main-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-upper_gi_bleeding.csv

  make_model_input-cohort_vax-main-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-variceal_gi_bleeding.rds

  describe_model_input-cohort_vax-main-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-variceal_gi_bleeding.txt

  cox_ipw-cohort_vax-main-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-main-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-variceal_gi_bleeding.csv

  make_model_input-cohort_vax-main-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_vax-main-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-main-vomiting.rds

  describe_model_input-cohort_vax-main-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-main-vomiting rds
    needs:
    - make_model_input-cohort_vax-main-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-main-vomiting.txt

  cox_ipw-cohort_vax-main-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-main-vomiting.rds --ipw=TRUE
      --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-main-vomiting.csv
    needs:
    - make_model_input-cohort_vax-main-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-main-vomiting.csv

  make_model_input-cohort_prevax-sub_age_18_39-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_18_39-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_18_39-diarrhoea.rds

  describe_model_input-cohort_prevax-sub_age_18_39-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_18_39-diarrhoea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_age_18_39-diarrhoea.txt

  cox_ipw-cohort_prevax-sub_age_18_39-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_18_39-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_18_39-diarrhoea.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_18_39-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_18_39-diarrhoea.csv

  make_model_input-cohort_unvax-sub_age_18_39-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_18_39-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_18_39-diarrhoea.rds

  describe_model_input-cohort_unvax-sub_age_18_39-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_18_39-diarrhoea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_age_18_39-diarrhoea.txt

  cox_ipw-cohort_unvax-sub_age_18_39-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_18_39-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_18_39-diarrhoea.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_18_39-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_18_39-diarrhoea.csv

  make_model_input-cohort_vax-sub_age_18_39-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_18_39-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_18_39-diarrhoea.rds

  describe_model_input-cohort_vax-sub_age_18_39-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_18_39-diarrhoea
      rds
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_age_18_39-diarrhoea.txt

  cox_ipw-cohort_vax-sub_age_18_39-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_18_39-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_18_39-diarrhoea.csv
    needs:
    - make_model_input-cohort_vax-sub_age_18_39-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_18_39-diarrhoea.csv

  make_model_input-cohort_prevax-sub_age_40_59-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_40_59-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_40_59-diarrhoea.rds

  describe_model_input-cohort_prevax-sub_age_40_59-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_40_59-diarrhoea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_age_40_59-diarrhoea.txt

  cox_ipw-cohort_prevax-sub_age_40_59-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_40_59-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_40_59-diarrhoea.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_40_59-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_40_59-diarrhoea.csv

  make_model_input-cohort_unvax-sub_age_40_59-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_40_59-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_40_59-diarrhoea.rds

  describe_model_input-cohort_unvax-sub_age_40_59-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_40_59-diarrhoea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_age_40_59-diarrhoea.txt

  cox_ipw-cohort_unvax-sub_age_40_59-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_40_59-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_40_59-diarrhoea.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_40_59-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_40_59-diarrhoea.csv

  make_model_input-cohort_vax-sub_age_40_59-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_40_59-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_40_59-diarrhoea.rds

  describe_model_input-cohort_vax-sub_age_40_59-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_40_59-diarrhoea
      rds
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_age_40_59-diarrhoea.txt

  cox_ipw-cohort_vax-sub_age_40_59-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_40_59-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_40_59-diarrhoea.csv
    needs:
    - make_model_input-cohort_vax-sub_age_40_59-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_40_59-diarrhoea.csv

  make_model_input-cohort_prevax-sub_age_60_79-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_60_79-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_60_79-diarrhoea.rds

  describe_model_input-cohort_prevax-sub_age_60_79-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_60_79-diarrhoea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_age_60_79-diarrhoea.txt

  cox_ipw-cohort_prevax-sub_age_60_79-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_60_79-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_60_79-diarrhoea.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_60_79-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_60_79-diarrhoea.csv

  make_model_input-cohort_unvax-sub_age_60_79-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_60_79-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_60_79-diarrhoea.rds

  describe_model_input-cohort_unvax-sub_age_60_79-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_60_79-diarrhoea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_age_60_79-diarrhoea.txt

  cox_ipw-cohort_unvax-sub_age_60_79-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_60_79-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_60_79-diarrhoea.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_60_79-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_60_79-diarrhoea.csv

  make_model_input-cohort_vax-sub_age_60_79-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_60_79-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_60_79-diarrhoea.rds

  describe_model_input-cohort_vax-sub_age_60_79-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_60_79-diarrhoea
      rds
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_age_60_79-diarrhoea.txt

  cox_ipw-cohort_vax-sub_age_60_79-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_60_79-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_60_79-diarrhoea.csv
    needs:
    - make_model_input-cohort_vax-sub_age_60_79-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_60_79-diarrhoea.csv

  make_model_input-cohort_prevax-sub_age_80_110-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_age_80_110-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_age_80_110-diarrhoea.rds

  describe_model_input-cohort_prevax-sub_age_80_110-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_age_80_110-diarrhoea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_age_80_110-diarrhoea.txt

  cox_ipw-cohort_prevax-sub_age_80_110-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_age_80_110-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_prevax-sub_age_80_110-diarrhoea.csv
    needs:
    - make_model_input-cohort_prevax-sub_age_80_110-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_age_80_110-diarrhoea.csv

  make_model_input-cohort_unvax-sub_age_80_110-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_age_80_110-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_age_80_110-diarrhoea.rds

  describe_model_input-cohort_unvax-sub_age_80_110-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_age_80_110-diarrhoea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_age_80_110-diarrhoea.txt

  cox_ipw-cohort_unvax-sub_age_80_110-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_age_80_110-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_unvax-sub_age_80_110-diarrhoea.csv
    needs:
    - make_model_input-cohort_unvax-sub_age_80_110-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_age_80_110-diarrhoea.csv

  make_model_input-cohort_vax-sub_age_80_110-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_age_80_110-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_age_80_110-diarrhoea.rds

  describe_model_input-cohort_vax-sub_age_80_110-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_age_80_110-diarrhoea
      rds
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_age_80_110-diarrhoea.txt

  cox_ipw-cohort_vax-sub_age_80_110-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_age_80_110-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=FALSE --df_output=model_output-cohort_vax-sub_age_80_110-diarrhoea.csv
    needs:
    - make_model_input-cohort_vax-sub_age_80_110-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_age_80_110-diarrhoea.csv

  make_model_input-cohort_unvax-sub_covid_history-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-abdominal_distension.rds

  describe_model_input-cohort_unvax-sub_covid_history-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-abdominal_distension.txt

  cox_ipw-cohort_unvax-sub_covid_history-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-abdominal_distension.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-abdominal_distension.csv

  make_model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort.rds

  describe_model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort.txt

  cox_ipw-cohort_unvax-sub_covid_history-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-abdominal_paindiscomfort.csv

  make_model_input-cohort_unvax-sub_covid_history-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-acute_pancreatitis.rds

  describe_model_input-cohort_unvax-sub_covid_history-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-acute_pancreatitis.txt

  cox_ipw-cohort_unvax-sub_covid_history-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-acute_pancreatitis.csv

  make_model_input-cohort_unvax-sub_covid_history-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-appendicitis.rds

  describe_model_input-cohort_unvax-sub_covid_history-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-appendicitis
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-appendicitis.txt

  cox_ipw-cohort_unvax-sub_covid_history-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-appendicitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-appendicitis.csv

  make_model_input-cohort_unvax-sub_covid_history-belching:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-belching.rds

  describe_model_input-cohort_unvax-sub_covid_history-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-belching
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-belching.txt

  cox_ipw-cohort_unvax-sub_covid_history-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-belching.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-belching.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-belching.csv

  make_model_input-cohort_unvax-sub_covid_history-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-bloody_stools.rds

  describe_model_input-cohort_unvax-sub_covid_history-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-bloody_stools
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-bloody_stools.txt

  cox_ipw-cohort_unvax-sub_covid_history-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-bloody_stools.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-bloody_stools.csv

  make_model_input-cohort_unvax-sub_covid_history-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-bowel_ischaemia.rds

  describe_model_input-cohort_unvax-sub_covid_history-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-bowel_ischaemia.txt

  cox_ipw-cohort_unvax-sub_covid_history-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-bowel_ischaemia.csv

  make_model_input-cohort_unvax-sub_covid_history-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-diarrhoea.rds

  describe_model_input-cohort_unvax-sub_covid_history-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-diarrhoea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-diarrhoea.txt

  cox_ipw-cohort_unvax-sub_covid_history-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-diarrhoea.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-diarrhoea.csv

  make_model_input-cohort_unvax-sub_covid_history-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-dyspepsia.rds

  describe_model_input-cohort_unvax-sub_covid_history-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-dyspepsia
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-dyspepsia.txt

  cox_ipw-cohort_unvax-sub_covid_history-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-dyspepsia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-dyspepsia.csv

  make_model_input-cohort_unvax-sub_covid_history-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-gallstones_disease.rds

  describe_model_input-cohort_unvax-sub_covid_history-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-gallstones_disease.txt

  cox_ipw-cohort_unvax-sub_covid_history-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-gallstones_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-gallstones_disease.csv

  make_model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_unvax-sub_covid_history-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-ibs.rds

  describe_model_input-cohort_unvax-sub_covid_history-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-ibs
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-ibs.txt

  cox_ipw-cohort_unvax-sub_covid_history-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-ibs.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-ibs.csv

  make_model_input-cohort_unvax-sub_covid_history-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-intestinal_obstruction.rds

  describe_model_input-cohort_unvax-sub_covid_history-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-intestinal_obstruction.txt

  cox_ipw-cohort_unvax-sub_covid_history-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-intestinal_obstruction.csv

  make_model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_history-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-lower_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_history-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-nausea.rds

  describe_model_input-cohort_unvax-sub_covid_history-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-nausea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-nausea.txt

  cox_ipw-cohort_unvax-sub_covid_history-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-nausea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-nausea.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-nausea.csv

  make_model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_history-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-peptic_ulcer.rds

  describe_model_input-cohort_unvax-sub_covid_history-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-peptic_ulcer.txt

  cox_ipw-cohort_unvax-sub_covid_history-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-peptic_ulcer.csv

  make_model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_history-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-upper_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_history-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-variceal_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_history-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_history-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_history-vomiting.rds

  describe_model_input-cohort_unvax-sub_covid_history-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_history-vomiting
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_history-vomiting.txt

  cox_ipw-cohort_unvax-sub_covid_history-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_history-vomiting.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_history-vomiting.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_history-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_history-vomiting.csv

  make_model_input-cohort_vax-sub_covid_history-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-abdominal_distension.rds

  describe_model_input-cohort_vax-sub_covid_history-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-abdominal_distension.txt

  cox_ipw-cohort_vax-sub_covid_history-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-abdominal_distension.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-abdominal_distension.csv

  make_model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort.rds

  describe_model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort.txt

  cox_ipw-cohort_vax-sub_covid_history-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-abdominal_paindiscomfort.csv

  make_model_input-cohort_vax-sub_covid_history-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-acute_pancreatitis.rds

  describe_model_input-cohort_vax-sub_covid_history-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-acute_pancreatitis.txt

  cox_ipw-cohort_vax-sub_covid_history-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-acute_pancreatitis.csv

  make_model_input-cohort_vax-sub_covid_history-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-appendicitis.rds

  describe_model_input-cohort_vax-sub_covid_history-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-appendicitis
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-appendicitis.txt

  cox_ipw-cohort_vax-sub_covid_history-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-appendicitis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-appendicitis.csv

  make_model_input-cohort_vax-sub_covid_history-belching:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-belching.rds

  describe_model_input-cohort_vax-sub_covid_history-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-belching
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-belching.txt

  cox_ipw-cohort_vax-sub_covid_history-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-belching.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-belching.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-belching.csv

  make_model_input-cohort_vax-sub_covid_history-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-bloody_stools.rds

  describe_model_input-cohort_vax-sub_covid_history-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-bloody_stools
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-bloody_stools.txt

  cox_ipw-cohort_vax-sub_covid_history-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-bloody_stools.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-bloody_stools.csv

  make_model_input-cohort_vax-sub_covid_history-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-bowel_ischaemia.rds

  describe_model_input-cohort_vax-sub_covid_history-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-bowel_ischaemia.txt

  cox_ipw-cohort_vax-sub_covid_history-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-bowel_ischaemia.csv

  make_model_input-cohort_vax-sub_covid_history-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-diarrhoea.rds

  describe_model_input-cohort_vax-sub_covid_history-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-diarrhoea
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-diarrhoea.txt

  cox_ipw-cohort_vax-sub_covid_history-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-diarrhoea.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-diarrhoea.csv

  make_model_input-cohort_vax-sub_covid_history-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-dyspepsia.rds

  describe_model_input-cohort_vax-sub_covid_history-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-dyspepsia
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-dyspepsia.txt

  cox_ipw-cohort_vax-sub_covid_history-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-dyspepsia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-dyspepsia.csv

  make_model_input-cohort_vax-sub_covid_history-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-gallstones_disease.rds

  describe_model_input-cohort_vax-sub_covid_history-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-gallstones_disease.txt

  cox_ipw-cohort_vax-sub_covid_history-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-gallstones_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-gallstones_disease.csv

  make_model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_vax-sub_covid_history-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-ibs.rds

  describe_model_input-cohort_vax-sub_covid_history-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-ibs
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-ibs.txt

  cox_ipw-cohort_vax-sub_covid_history-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-ibs.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-ibs.csv

  make_model_input-cohort_vax-sub_covid_history-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-intestinal_obstruction.rds

  describe_model_input-cohort_vax-sub_covid_history-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-intestinal_obstruction.txt

  cox_ipw-cohort_vax-sub_covid_history-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-intestinal_obstruction.csv

  make_model_input-cohort_vax-sub_covid_history-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-lower_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_history-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-lower_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_history-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-lower_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_history-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-nausea.rds

  describe_model_input-cohort_vax-sub_covid_history-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-nausea
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-nausea.txt

  cox_ipw-cohort_vax-sub_covid_history-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-nausea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-nausea.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-nausea.csv

  make_model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_history-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-peptic_ulcer.rds

  describe_model_input-cohort_vax-sub_covid_history-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-peptic_ulcer.txt

  cox_ipw-cohort_vax-sub_covid_history-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-peptic_ulcer.csv

  make_model_input-cohort_vax-sub_covid_history-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-upper_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_history-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-upper_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_history-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-upper_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_history-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-variceal_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_history-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_history-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_history-vomiting.rds

  describe_model_input-cohort_vax-sub_covid_history-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_history-vomiting
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_history-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_history-vomiting.txt

  cox_ipw-cohort_vax-sub_covid_history-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_history-vomiting.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_history-vomiting.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_history-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_history-vomiting.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-abdominal_distension.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-abdominal_distension.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-abdominal_paindiscomfort.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-acute_pancreatitis.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-appendicitis.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-appendicitis
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-appendicitis.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-appendicitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-appendicitis.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-belching:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-belching.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-belching
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-belching.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-belching.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-belching.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-belching.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-bloody_stools.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-bloody_stools.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-bowel_ischaemia.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-diarrhoea.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-diarrhoea.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-dyspepsia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-dyspepsia.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-gallstones_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-gallstones_disease.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-ibs.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-ibs
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-ibs.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-ibs.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-ibs.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-intestinal_obstruction.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-lower_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-nausea.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-nausea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-nausea.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-nausea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-nausea.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-nausea.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-peptic_ulcer.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-upper_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-variceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_hospitalised-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_hospitalised-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_hospitalised-vomiting.rds

  describe_model_input-cohort_prevax-sub_covid_hospitalised-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_hospitalised-vomiting
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_hospitalised-vomiting.txt

  cox_ipw-cohort_prevax-sub_covid_hospitalised-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_hospitalised-vomiting.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_hospitalised-vomiting.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_hospitalised-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_hospitalised-vomiting.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-abdominal_distension.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-abdominal_distension.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-abdominal_paindiscomfort.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-acute_pancreatitis.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-appendicitis.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-appendicitis
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-appendicitis.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-appendicitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-appendicitis.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-belching:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-belching.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-belching
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-belching.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-belching.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-belching.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-belching.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-bloody_stools.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-bloody_stools.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-bowel_ischaemia.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-diarrhoea.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-diarrhoea.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-dyspepsia.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-dyspepsia.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-gallstones_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-gallstones_disease.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-ibs.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-ibs
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-ibs.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-ibs.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-ibs.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-intestinal_obstruction.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-lower_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-nausea.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-nausea
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-nausea.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-nausea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-nausea.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-nausea.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-peptic_ulcer.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-upper_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-variceal_gi_bleeding.csv

  make_model_input-cohort_unvax-sub_covid_hospitalised-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_hospitalised-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_hospitalised-vomiting.rds

  describe_model_input-cohort_unvax-sub_covid_hospitalised-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_hospitalised-vomiting
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_unvax-sub_covid_hospitalised-vomiting.txt

  cox_ipw-cohort_unvax-sub_covid_hospitalised-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_unvax-sub_covid_hospitalised-vomiting.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_unvax-sub_covid_hospitalised-vomiting.csv
    needs:
    - make_model_input-cohort_unvax-sub_covid_hospitalised-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_unvax-sub_covid_hospitalised-vomiting.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-abdominal_distension.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-abdominal_distension.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-abdominal_paindiscomfort.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-acute_pancreatitis.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-appendicitis.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-appendicitis
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-appendicitis.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-appendicitis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-appendicitis.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-belching:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-belching.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-belching
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-belching.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-belching.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-belching.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-belching.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-bloody_stools.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-bloody_stools
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-bloody_stools.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-bloody_stools.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-bloody_stools.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-bowel_ischaemia.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-diarrhoea.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-diarrhoea
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-diarrhoea.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-diarrhoea.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-diarrhoea.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-dyspepsia.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-dyspepsia
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-dyspepsia.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-dyspepsia.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-dyspepsia.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-gallstones_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-gallstones_disease.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-ibs.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-ibs
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-ibs.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-ibs.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-ibs.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-intestinal_obstruction.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-lower_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-nausea.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-nausea
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-nausea.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-nausea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-nausea.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-nausea.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-peptic_ulcer.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-upper_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-variceal_gi_bleeding.csv

  make_model_input-cohort_vax-sub_covid_hospitalised-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_vax-sub_covid_hospitalised-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_vax-sub_covid_hospitalised-vomiting.rds

  describe_model_input-cohort_vax-sub_covid_hospitalised-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_vax-sub_covid_hospitalised-vomiting
      rds
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_vax-sub_covid_hospitalised-vomiting.txt

  cox_ipw-cohort_vax-sub_covid_hospitalised-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_vax-sub_covid_hospitalised-vomiting.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2021-06-01 --study_stop=2021-12-14
      --cut_points=28;197 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_vax-sub_covid_hospitalised-vomiting.csv
    needs:
    - make_model_input-cohort_vax-sub_covid_hospitalised-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_vax-sub_covid_hospitalised-vomiting.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-abdominal_distension.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-abdominal_paindiscomfort.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-acute_pancreatitis.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-appendicitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-appendicitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-appendicitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-appendicitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-appendicitis.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-belching:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-belching
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-belching.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-belching:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-belching
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-belching
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-belching.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-belching:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-belching.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-belching.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-belching
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-belching.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-bloody_stools
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-bloody_stools:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-bloody_stools.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-bloody_stools
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-bloody_stools.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-bowel_ischaemia.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-diarrhoea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-diarrhoea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-diarrhoea.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-diarrhoea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-diarrhoea.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-dyspepsia
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-dyspepsia:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-dyspepsia.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-dyspepsia
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-dyspepsia.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-gallstones_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-gallstones_disease.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-gastro_oesophageal_reflux_disease.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-ibs:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-ibs
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-ibs.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-ibs:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-ibs
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-ibs
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-ibs.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-ibs:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-ibs.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-ibs.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-ibs
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-ibs.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-intestinal_obstruction.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-lower_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-nausea:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-nausea
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-nausea.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-nausea:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-nausea
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-nausea
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-nausea.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-nausea:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-nausea.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-nausea.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-nausea
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-nausea.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-nonalcoholic_steatohepatitis.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-nonvariceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-peptic_ulcer.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-upper_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-variceal_gi_bleeding.csv

  make_model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting:
    run: r:latest analysis/model/make_model_input.R cohort_prevax-sub_covid_nonhospitalised-vomiting
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting.rds

  describe_model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting:
    run: r:latest analysis/describe_file.R model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting
      rds
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting
    outputs:
      moderately_sensitive:
        describe_model_input: output/describe-model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting.txt

  cox_ipw-cohort_prevax-sub_covid_nonhospitalised-vomiting:
    run: cox-ipw:v0.0.20 --df_input=model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting.rds
      --ipw=TRUE --exposure=exp_date --outcome=out_date --strata=cov_cat_region --covariate_sex=cov_cat_sex
      --covariate_age=cov_num_age --covariate_other=cov_cat_ethnicity;cov_cat_deprivation;cov_cat_smoking_status;cov_bin_carehome_status;cov_num_consulation_rate;cov_bin_healthcare_worker;cov_bin_gi_operations;cov_bin_overall_gi_and_symptoms;cov_bin_obesity;cov_bin_antidepressants_bnf;cov_bin_alcohol_above_limits;cov_bin_cholelisthiasis;cov_bin_h_pylori_infection;cov_bin_nsaid_bnf;cov_bin_aspirin_bnf;
      --cox_start=index_date --cox_stop=end_date --study_start=2020-01-01 --study_stop=2021-06-01
      --cut_points=28;197;535 --controls_per_case=20 --total_event_threshold=50 --episode_event_threshold=5
      --covariate_threshold=5 --age_spline=TRUE --df_output=model_output-cohort_prevax-sub_covid_nonhospitalised-vomiting.csv
    needs:
    - make_model_input-cohort_prevax-sub_covid_nonhospitalised-vomiting
    outputs:
      moderately_sensitive:
        model_output: output/model_output-cohort_prevax-sub_covid_nonhospitalised-vomiting.csv

  make_model_input-cohort_unvax-sub_covid_nonhospitalised-abdominal_distension:
    run: r:latest analysis/model/make_model_input.R cohort_unvax-sub_covid_nonhospitalised-abdominal_distension
    needs:
    - stage1_data_cleaning_all
    outputs:
      highly_sensitive:
        model_input: output/model_input-cohort_unvax-sub_covid_nonhospitalised-abdominal_distension.rds

  describe_model_input-cohort_unvax-sub_covid_nonhospitalised-abdominal_distension:
    run: r:latest analysis/describe_file.R model_input-cohort_unvax-sub_covid_nonhospitalised-abdominal_distension
      rds
    needs:
    - make_model_input-cohort_unvax-sub_covid_nonhospitalised-abdominal_